<emd emdb_id="EMD-5258" version="3.0.1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_1_1/emdb_relaxed.xsd">
    <admin>
        <current_status>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2011-02-10</deposition>
            <header_release>2011-05-11</header_release>
            <map_release>2011-05-11</map_release>
            <update>2014-05-07</update>
        </key_dates>
        <title>Lidless D386A Mm-cpn in the pre-hydrolysis ATP-bound state</title>
        <authors_list>
            <author>Zhang J</author>
            <author>Ma B</author>
            <author>DiMaio F</author>
            <author>Douglas NR</author>
            <author>Joachimiak L</author>
            <author>Baker D</author>
            <author>Frydman J</author>
            <author>Levitt M</author>
            <author>Chiu W</author>
        </authors_list>
        <keywords>Mm-cpn, Chaperonin, ATP-bound</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Zhang J</author>
                    <author order="2">Ma B</author>
                    <author order="3">DiMaio F</author>
                    <author order="4">Douglas NR</author>
                    <author order="5">Joachimiak LA</author>
                    <author order="6">Baker D</author>
                    <author order="7">Frydman J</author>
                    <author order="8">Levitt M</author>
                    <author order="9">Chiu W</author>
                    <title>Cryo-EM structure of a group II chaperonin in the prehydrolysis ATP-bound state leading to lid closure.</title>
                    <journal>STRUCTURE</journal>
                    <volume>19</volume>
                    <first_page>633</first_page>
                    <last_page>639</last_page>
                    <year>2011</year>
                    <external_references type="PUBMED">21565698</external_references>
                    <external_references type="DOI">doi:10.1016/j.str.2011.03.005</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>3j02</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Lidless D386A Mm-cpn variant</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Lidless D386A Mm-cpn variant</name>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">1</experimental>
                    <theoretical units="MDa">1</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="Mm-cpn">Methanococcus maripaludis chaperonin</name>
                <natural_source database="NCBI">
                    <organism ncbi="39152">Methanococcus maripaludis</organism>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">1</experimental>
                    <theoretical units="MDa">1</theoretical>
                </molecular_weight>
                <details>incubated with 1mM ATP</details>
                <number_of_copies>1</number_of_copies>
                <oligomeric_state>16-mer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <sequence />
            </protein_or_peptide>
        </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">
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <instrument>OTHER</instrument>
                        <details>Vitrification instrument: vitrobot</details>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>JEOL 2200FS</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>
                    <nominal_defocus_min units="&#181;m">1.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">2.5</nominal_defocus_max>
                    <nominal_magnification>80000.0</nominal_magnification>
                    <calibrated_magnification>112000.0</calibrated_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <specialist_optics>
                        <energy_filter>
                            <name>in-column omega energy filter</name>
                            <lower_energy_threshold units="eV">0.0</lower_energy_threshold>
                            <upper_energy_threshold units="eV">10.0</upper_energy_threshold>
                        </energy_filter>
                    </specialist_optics>
                    <date>2009-09-08</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GENERIC GATAN (4k x 4k)</film_or_detector_model>
                            <number_real_images>64</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">20</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Gatan side entry</specimen_holder>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <ctf_correction>
                    <details>Each CCD image</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">8.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN</name>
                        </software>
                    </software_list>
                    <number_images_used>12761</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="54001">
        <file>emd_5258.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>240</col>
            <row>240</row>
            <sec>240</sec>
        </dimensions>
        <origin>
            <col>-120</col>
            <row>-120</row>
            <sec>-120</sec>
        </origin>
        <spacing>
            <x>240</x>
            <y>240</y>
            <z>240</z>
        </spacing>
        <cell>
            <a units="&#8491;">340.8</a>
            <b units="&#8491;">340.8</b>
            <c units="&#8491;">340.8</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>-0.12193819</minimum>
            <maximum>0.23173273</maximum>
            <average>0.00300522</average>
            <std>0.01658083</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.42</x>
            <y units="&#8491;">1.42</y>
            <z units="&#8491;">1.42</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.02</level>
                <source>EMDB</source>
            </contour>
        </contour_list>
        <annotation_details>This is the density map of lidless D386A Mm-cpn in the pre-hydrolysis ATP-bound state.</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5258::::</details>
    </map>
</emd>