<?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_9_3/emdb.xsd" version="3.0.9.3" emdb_id="EMD-21109">
    <admin>
        <current_status>
            <date>2024-10-16</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2019-12-11</deposition>
            <header_release>2020-01-15</header_release>
            <map_release>2020-08-12</map_release>
            <update>2024-10-16</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)</funding_body>
                <code>5T32GM008496</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Science Foundation (NSF, United States)</funding_body>
                <code>DMR-1548924</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Department of Energy (DOE, United States)</funding_body>
                <code>DE-FC02-02ER63421</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>R35 GM128867</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Sao Paulo Research Foundation (FAPESP)</funding_body>
                <code>16/24191-8</code>
                <country>Brazil</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Sao Paulo Research Foundation (FAPESP)</funding_body>
                <code>17/13485-3</code>
                <country>Brazil</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Spanish Ministry of Economy and Competitiveness</funding_body>
                <code>BIO2015-64216-P</code>
                <country>Spain</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Spanish Ministry of Economy and Competitiveness</funding_body>
                <code>PGC2018-101370-B-100</code>
                <country>Spain</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Spanish Ministry of Economy and Competitiveness</funding_body>
                <code>MDM2014-0435-01</code>
                <country>Spain</country>
            </grant_reference>
        </grant_support>
        <title>Proteinase K Determined by MicroED Phased by ARCIMBOLDO_SHREDDER</title>
        <authors_list>
            <author>Richards LS</author>
            <author>Martynowycz MW</author>
        </authors_list>
        <keywords>ARCIMBOLDO, MicroED, HYDROLASE</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author ORCID="0000-0002-1694-1652" order="1">Richards LR</author>
                    <author ORCID="0000-0002-9283-2220" order="2">Millan C</author>
                    <author order="3">Miao J</author>
                    <author ORCID="0000-0003-0055-230X" order="4">Martynowycz MW</author>
                    <author ORCID="0000-0003-0874-9043" order="5">Sawaya MR</author>
                    <author ORCID="0000-0002-9254-4069" order="6">Gonen T</author>
                    <author order="7">Borges RJ</author>
                    <author ORCID="0000-0003-2504-1696" order="8">Uson I</author>
                    <author ORCID="0000-0001-8471-2504" order="9">Rodriguez JA</author>
                    <title>Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER</title>
                    <journal_abbreviation>Acta Crystallogr.,Sect.D</journal_abbreviation>
                    <country>US</country>
                    <volume>76</volume>
                    <first_page>703</first_page>
                    <last_page>712</last_page>
                    <year>2020</year>
                    <external_references type="DOI">doi:10.1107/S2059798320008049</external_references>
                    <external_references type="ISSN">1399-0047</external_references>
                    <external_references type="ASTM">ABCRE6</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>6v8r</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Proteinase K</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Proteinase K</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="37998">Parengyodontium album</organism>
                </natural_source>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Proteinase K</name>
                <natural_source database="NCBI">
                    <organism ncbi="37998">Parengyodontium album</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.028958791</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="37998">Parengyodontium album</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>AAQTNAPWGLARISSTSPGTSTYYYDESAGQGSCVYVIDTGIEASHPEFEGRAQMVKTYYYSSRDGNGHGTHCAGTVGSR
TYGVAKKTQLFGVKVLDDNGSGQYSTIIAGMDFVASDKNNRNCPKGVVASLSLGGGYSSSVNSAAARLQSSGVMVAVAAG
NNNADARNYSPASEPSVCTVGASDRYDRRSSFSNYGSVLDIFGPGTDILSTWIGGSTRSISGTSMATPHVAGLAAYLMTL
GKTTAASACRYIADTANKGDLSNIPFGTVNLLAYNNYQA</string>
                    <external_references type="UNIPROTKB">P06873</external_references>
                </sequence>
                <ec_number>3.4.21.64</ec_number>
            </protein_or_peptide>
            <ligand macromolecule_id="2">
                <name>CALCIUM ION</name>
                <molecular_weight>
                    <theoretical units="MDa">4.0078e-05</theoretical>
                </molecular_weight>
                <number_of_copies>2</number_of_copies>
                <formula>CA</formula>
            </ligand>
            <ligand macromolecule_id="3">
                <name>water</name>
                <molecular_weight>
                    <theoretical units="MDa">1.8015e-05</theoretical>
                </molecular_weight>
                <number_of_copies>121</number_of_copies>
                <formula>HOH</formula>
            </ligand>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>electronCrystallography</method>
            <aggregation_state>threeDArray</aggregation_state>
            <specimen_preparation_list>
                <crystallography_preparation preparation_id="1">
                    <concentration units="mg/mL">40</concentration>
                    <buffer>
                        <ph>8.0</ph>
                        <component>
                            <concentration units="mM">100.0</concentration>
                            <name>Tris-HCl</name>
                        </component>
                        <component>
                            <concentration units="M">1.25</concentration>
                            <name>ammonium sulfate</name>
                        </component>
                    </buffer>
                    <grid>
                        <model>Quantifoil R2/2</model>
                        <material>COPPER</material>
                        <mesh>300</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>HOLEY ARRAY</film_topology>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                    </vitrification>
                    <details>Crystal</details>
                </crystallography_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <crystallography_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI 20</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>DIFFRACTION</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">200</acceleration_voltage>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>TVIPS TEMCAM-F416 (4k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/Å^2">1.0</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <camera_length units="mm">1200</camera_length>
                </crystallography_microscopy>
            </microscopy_list>
            <crystallography_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <final_reconstruction>
                    <resolution_method>DIFFRACTION PATTERN/LAYERLINES</resolution_method>
                </final_reconstruction>
                <crystallography_statistics>
                    <number_intensities_measured>194052</number_intensities_measured>
                    <number_structure_factors>29061</number_structure_factors>
                    <fourier_space_coverage>93.900000000000006</fourier_space_coverage>
                    <r_sym>0.353</r_sym>
                    <r_merge>0.353</r_merge>
                    <overall_phase_error>23.92</overall_phase_error>
                    <overall_phase_residual>0.01</overall_phase_residual>
                    <phase_error_rejection_criteria>0</phase_error_rejection_criteria>
                    <high_resolution units="Å">1.6</high_resolution>
                    <shell_list>
                        <shell shell_id="1">
                            <high_resolution units="Å">55.79</high_resolution>
                            <low_resolution units="Å">1.6</low_resolution>
                            <number_structure_factors>29061</number_structure_factors>
                            <phase_residual>0.01</phase_residual>
                            <fourier_space_coverage>93.900000000000006</fourier_space_coverage>
                            <multiplicity>6.68</multiplicity>
                        </shell>
                    </shell_list>
                </crystallography_statistics>
            </crystallography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="3821">
        <file>emd_21109.map.gz</file>
        <symmetry>
            <space_group>96</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>97</col>
            <row>107</row>
            <sec>92</sec>
        </dimensions>
        <origin>
            <col>41</col>
            <row>-21</row>
            <sec>-44</sec>
        </origin>
        <spacing>
            <x>128</x>
            <y>128</y>
            <z>176</z>
        </spacing>
        <cell>
            <a units="Å">67.24992</a>
            <b units="Å">67.24992</b>
            <c units="Å">99.92048</c>
            <alpha units="deg">90.0</alpha>
            <beta units="deg">90.0</beta>
            <gamma units="deg">90.0</gamma>
        </cell>
        <axis_order>
            <fast>Y</fast>
            <medium>X</medium>
            <slow>Z</slow>
        </axis_order>
        <statistics>
            <minimum>-0.92665446</minimum>
            <maximum>2.960122</maximum>
            <average>-0.0002680721</average>
            <std>0.3668702</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">0.52539</x>
            <y units="Å">0.52539</y>
            <z units="Å">0.56773</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.8</level>
                <source>EMDB</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-21109::::</label>
        <annotation_details>Proteinase K</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <refinement_protocol>OTHER</refinement_protocol>
                <refinement_space>RECIPROCAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
