<?xml version="1.0" encoding="UTF-8"?>
<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="https://ftp.ebi.ac.uk/pub/databases/em_ebi/emdb_related/emdb-schemas/emdb_schemas/v3/v3_0_11_7/emdb.xsd" version="3.0.11.7" emdb_id="EMD-23773">
    <admin>
        <current_status>
            <date>2026-08-12</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <revision_history>
            <revision version="1.0" date="2022-01-05">
                <change_list>
                    <model>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </model>
                    <metadata>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </metadata>
                </change_list>
            </revision>
            <revision version="1.1" date="2026-08-12">
                <change_list>
                    <metadata>
                        <revision_group>EXPERIMENTAL_SUMMARY</revision_group>
                        <categories>
                            <category>em_admin</category>
                        </categories>
                        <items>
                            <item>_em_admin.last_update</item>
                        </items>
                    </metadata>
                </change_list>
            </revision>
            <revision version="1.2" date="2026-08-12">
                <change_list>
                    <model>
                        <revision_type>REMEDIATION</revision_type>
                        <provider>REPOSITORY</provider>
                        <description>Metalloprotein remediation</description>
                        <revision_group>STRUCTURE_SUMMARY</revision_group>
                        <categories>
                            <category>em_admin</category>
                            <category>pdbx_entry_details</category>
                            <category>pdbx_modification_feature</category>
                            <category>pdbx_nonpoly_atom_coordination</category>
                            <category>pdbx_nonpoly_atom_coordination_sphere</category>
                            <category>pdbx_nonpoly_atom_coordination_sphere_order</category>
                        </categories>
                        <items>
                            <item>_em_admin.last_update</item>
                            <item>_pdbx_entry_details.has_protein_modification</item>
                        </items>
                    </model>
                </change_list>
            </revision>
        </revision_history>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2021-04-05</deposition>
            <header_release>2022-01-05</header_release>
            <map_release>2022-01-05</map_release>
            <update>2026-08-12</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Science Foundation (NSF, United States)</funding_body>
                <code>2017246757</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)</funding_body>
                <code>GM126982</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)</funding_body>
                <code>5T32GM007287</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Howard Hughes Medical Institute (HHMI)</funding_body>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>Structure of the Neisseria gonorrhoeae ribonucleotide reductase in the inactive state</title>
        <authors_list>
            <author>Levitz TS</author>
            <author>Drennan CL</author>
        </authors_list>
        <keywords>inactive complex, ribonucleotide reductase, OXIDOREDUCTASE</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Levitz TS</author>
                    <author order="2">Brignole EJ</author>
                    <author order="3">Fong I</author>
                    <author order="4">Darrow MC</author>
                    <author order="5">Drennan CL</author>
                    <title>Effects of chameleon dispense-to-plunge speed on particle concentration, complex formation, and final resolution: A case study using the Neisseria gonorrhoeae ribonucleotide reductase inactive complex.</title>
                    <journal_abbreviation>J.Struct.Biol.</journal_abbreviation>
                    <country>US</country>
                    <volume>214</volume>
                    <first_page>107825</first_page>
                    <last_page>107825</last_page>
                    <year>2021</year>
                    <external_references type="PUBMED">34906669</external_references>
                    <external_references type="DOI">doi:10.1016/j.jsb.2021.107825</external_references>
                    <external_references type="ISSN">1095-8657</external_references>
                    <external_references type="CSD">0803</external_references>
                    <external_references type="ASTM">JSBIEM</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>7mdi</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
        <other_db_list>
            <db_reference>
                <db_name>EMDB</db_name>
                <accession_id>EMD-23773</accession_id>
                <content_type>associated EM volume</content_type>
                <details>Structure of the Neisseria gonorrhoeae ribonucleotide reductase in the inactive state</details>
            </db_reference>
        </other_db_list>
    </crossreferences>
    <sample>
        <name>Ribonucleotide reductase inactive complex</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Ribonucleotide reductase inactive complex</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>2</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="485">Neisseria gonorrhoeae</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.528</theoretical>
                </molecular_weight>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Ribonucleoside-diphosphate reductase subunit alpha</name>
                <natural_source database="NCBI">
                    <organism ncbi="242231">Neisseria gonorrhoeae</organism>
                    <strain>ATCC 700825 / FA 1090</strain>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.08708134399999999</theoretical>
                </molecular_weight>
                <number_of_copies>4</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MGHHHHHHENLYFQMNTPTDLKVTKRDGRLEAIDLDKIHRVVTWAAEGLENVSVSQVELKSHIQFYNGIRTDDIHETIIK
AAADLISEDTPDYQYLAARLAIFHLRKIAYGEYEPPHLYNHVKKLTDAGKYDRHILEDYSREEFDELNAYIDHERDMSFS
YAAVKQLEGKYLVQNRVTRQIYETPQFLYVLVAMCLFSKYPKEARLDYVKRFYDAVSTFKVSLPTPIMSGVRTPTRQFSS
CVLIECDDSLDSINATTSAIVKYVSQRAGIGINAGRIRGLDSEIRGGEARHTGCIPFFKMFQAAVKSCSQGGVRGGAATL
FYPLWHIEAESLLVLKNNRGVEDNRIRQLDYGVQINRLLYTRLIKGGNITLFSPNEVSGLYEAFFADQDEFERLYTKYEQ
DPNIRKRIIPAADLFSTLMQERAGTGRIYIQNVDHCNTHSPFDPRVAPVHQSNLCMEIALPTKPLDNINDPDGEIALCTL
SAFNLGALNSLDELEGLADLTVRALDALLDYQGYPVEAARTSTMDRRSLGIGVINYAYYLAKNGVRYSDGSALGLTHRTF
EAIQYYLLKASANLAKEYGACTLFNQTVYSQGKLPIDTYKKDLDAVCGEPLHYDWESLRADIVKYGLRNSTLTALMPSET
SSQIANATNGIEPPRGLVTVKASKDGILKQVVPEFETLKNAYETLWQLPGNEGYLKLVGVMQKFVDQAISANTAYDPGKF
EGNKVSMKQMLKDLLTAYKYGVKTLYYHNTRDGADDTQTDIQDDGCAGGACKI</string>
                    <external_references type="UNIPROTKB">Q5F8Z6</external_references>
                </sequence>
                <ec_number>1.17.4.1</ec_number>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>Ribonucleoside-diphosphate reductase subunit beta</name>
                <natural_source database="NCBI">
                    <organism ncbi="242231">Neisseria gonorrhoeae</organism>
                    <strain>ATCC 700825 / FA 1090</strain>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.045107785000000004</theoretical>
                </molecular_weight>
                <number_of_copies>4</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MGHHHHHHENLYFQMSYSTFPKTKNDALKEPMFFGQPVNVARYDQQKYEVFEKLIEKQLSFFWRPEEIDVSRDRIDYANL
PEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLVSIPELETWVETWSFSETIHSRSYTHIIRNIVNDPSVVFDDIVENEY
ITARAEDIACYYDDLIEYTQYYNLLGEGVHNVGGKPVTVSLRGLKKKLYLCLMCVNVLEAIRFYVSFACSFAFAERELME
GNAKIIKDIARDEALHLTGTQHMLNLMRSGVDDPEMAEIAAELQDECFQLFKKAAEQEKEWAAYLFKDGSMIGLNKEILS
QYVEYITNLRMQAVGLPAGFEGANQNPIPWINAWLSSDNVQVAPQEVEISSYLIGQIDSEVNTDDLGDFEL</string>
                    <external_references type="UNIPROTKB">Q5F8Z5</external_references>
                </sequence>
                <ec_number>1.17.4.1</ec_number>
            </protein_or_peptide>
            <ligand macromolecule_id="3">
                <name>CYTIDINE-5'-DIPHOSPHATE</name>
                <molecular_weight>
                    <theoretical units="MDa">0.000403176</theoretical>
                </molecular_weight>
                <number_of_copies>4</number_of_copies>
                <formula>CDP</formula>
            </ligand>
            <ligand macromolecule_id="4">
                <name>2'-DEOXYADENOSINE 5'-TRIPHOSPHATE</name>
                <molecular_weight>
                    <theoretical units="MDa">0.000491182</theoretical>
                </molecular_weight>
                <number_of_copies>8</number_of_copies>
                <formula>DTP</formula>
            </ligand>
            <ligand macromolecule_id="5">
                <name>MAGNESIUM ION</name>
                <molecular_weight>
                    <theoretical units="MDa">2.4305e-05</theoretical>
                </molecular_weight>
                <number_of_copies>8</number_of_copies>
                <formula>MG</formula>
            </ligand>
            <ligand macromolecule_id="6">
                <name>MU-OXO-DIIRON</name>
                <molecular_weight>
                    <theoretical units="MDa">0.00012768899999999998</theoretical>
                </molecular_weight>
                <number_of_copies>4</number_of_copies>
                <formula>FEO</formula>
            </ligand>
            <ligand macromolecule_id="7">
                <name>water</name>
                <molecular_weight>
                    <theoretical units="MDa">1.8015e-05</theoretical>
                </molecular_weight>
                <number_of_copies>24</number_of_copies>
                <formula>HOH</formula>
            </ligand>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>singleParticle</method>
            <aggregation_state>particle</aggregation_state>
            <specimen_preparation_list>
                <single_particle_preparation preparation_id="1">
                    <concentration units="mg/mL">6</concentration>
                    <buffer>
                        <ph>7.6</ph>
                        <component>
                            <concentration units="mM">50.0</concentration>
                            <name>HEPES</name>
                        </component>
                        <component>
                            <concentration units="mM">15.0</concentration>
                            <name>Magnesium Chloride</name>
                        </component>
                        <component>
                            <concentration units="mM">1.0</concentration>
                            <name>EDTA</name>
                        </component>
                        <component>
                            <concentration units="percent">3.06</concentration>
                            <name>Glycerol</name>
                        </component>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <details>Plunged using the chameleon (SPT labtech)

Glow discharged at 12 mA for 250 s. </details>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TALOS ARCTICA</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">200</acceleration_voltage>
                    <c2_aperture_diameter units="µm">50.0</c2_aperture_diameter>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="µm">1.2</nominal_defocus_min>
                    <nominal_defocus_max units="µm">3.1</nominal_defocus_max>
                    <nominal_magnification>92000.0</nominal_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <alignment_procedure>
                        <coma_free/>
                    </alignment_procedure>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>FEI FALCON III (4k x 4k)</film_or_detector_model>
                            <number_grids_imaged>1</number_grids_imaged>
                            <number_real_images>620</number_real_images>
                            <average_exposure_time units="s">7.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">53.15</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <particle_selection>
                    <number_selected>55161</number_selected>
                </particle_selection>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>CTFFIND</name>
                            <version>4</version>
                        </software>
                    </software_list>
                    <type>PHASE FLIPPING AND AMPLITUDE CORRECTION</type>
                </ctf_correction>
                <startup_model type_of_model="NONE"/>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>D2</point_group>
                    </applied_symmetry>
                    <resolution units="Å" res_type="BY AUTHOR">4.3</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>3.0.8</version>
                        </software>
                    </software_list>
                    <number_images_used>50425</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>RANDOM ASSIGNMENT</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>3.0.8</version>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>3.0.8</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="62501">
        <file>emd_23773.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>250</col>
            <row>250</row>
            <sec>250</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>250</x>
            <y>250</y>
            <z>250</z>
        </spacing>
        <cell>
            <a units="Å">399.95</a>
            <b units="Å">399.95</b>
            <c units="Å">399.95</c>
            <alpha units="deg">90.0</alpha>
            <beta units="deg">90.0</beta>
            <gamma units="deg">90.0</gamma>
        </cell>
        <axis_order>
            <fast>X</fast>
            <medium>Y</medium>
            <slow>Z</slow>
        </axis_order>
        <statistics>
            <minimum>-0.27861944</minimum>
            <maximum>0.47411168</maximum>
            <average>0.000034120498</average>
            <std>0.02169597</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.5998</x>
            <y units="Å">1.5998</y>
            <z units="Å">1.5998</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.13</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-23773::::</label>
    </map>
</emd>
