<?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-10528">
    <admin>
        <current_status>
            <date>2024-05-22</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2019-12-05</deposition>
            <header_release>2019-12-18</header_release>
            <map_release>2020-04-22</map_release>
            <update>2024-05-22</update>
        </key_dates>
        <title>Structure of the chaperonin gp146 from the bacteriophage EL (Pseudomonas aeruginosa) in the apo state</title>
        <authors_list>
            <author>Bracher A</author>
            <author>Wang H</author>
        </authors_list>
        <keywords>molecular chaperone, ATPase, chaperonin, CHAPERONE</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Bracher A</author>
                    <author order="2">Paul SS</author>
                    <author order="3">Wang H</author>
                    <author order="4">Wischnewski N</author>
                    <author order="5">Hartl FU</author>
                    <author ORCID="0000-0001-8213-6742" order="6">Hayer-Hartl M</author>
                    <title>Structure and conformational cycle of a bacteriophage-encoded chaperonin.</title>
                    <journal_abbreviation>Plos One</journal_abbreviation>
                    <country>US</country>
                    <volume>15</volume>
                    <first_page>e0230090</first_page>
                    <last_page>e0230090</last_page>
                    <year>2020</year>
                    <external_references type="PUBMED">32339190</external_references>
                    <external_references type="DOI">doi:10.1371/journal.pone.0230090</external_references>
                    <external_references type="ISSN">1932-6203</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>6tmv</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>The chaperonin gp146 from the bacteriophage EL (Pseudomonas aeruginosa) in the apo state</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>The chaperonin gp146 from the bacteriophage EL (Pseudomonas aeruginosa) in the apo state</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="273133">Pseudomonas phage EL</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.864</theoretical>
                </molecular_weight>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Putative GroEL-like chaperonine protein</name>
                <natural_source database="NCBI">
                    <organism ncbi="273133">Pseudomonas phage EL</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.06176094099999999</theoretical>
                </molecular_weight>
                <number_of_copies>14</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="469008">Escherichia coli BL21(DE3)</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MSQTLLVHGKDAQGIIKQVLSEVYDAVTSTMGPNGQLVMIKNGVSTKTTKDGVTVARSIRFADEAHELVNRVITEPATKT
DEECGDGTTTTIMLTHALYHLFKDFPGFQHHRNIEDLVERVIQRLESMAIRVEVDDPRLYQVALTSSNQDEKLARLVSEL
YANNKGSYPDIELKEGVNFEDQIEQTTGRTIRMFYANPWFAKGHQGGVTELTGFTAFVIDRRIDKEDTQKLIDGVNHLVK
THKQHLALPILLIARSFEEAANSTLMQLNAAHPTLVEDGRPWLIPLSTPVGGAIGTSELQDIAVMLNAPMLSDVADLTKL
DTHSINGQHGQLELGGNRSILKSTTPKDEDRIEQHARGIEELLEGFSLSDKFSVRARYNERRIRTLRGKLITISVGGETY
SEVKERVDRYEDVVKAIRSALENGILPGGGVSLVKAVFGTIKEGLEDKDQSAEFAKRYINSGIANELMRLSTIQHKLLFK
DTALYKENGSFHFNDDWLNTPTVMNLATGEIGTPEGLGIYDTAYASITALKGGLQTAKILATTKTLILGEKLSAVKVR</string>
                    <external_references type="UNIPROTKB">Q2Z0T5</external_references>
                </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">
                    <concentration units="mg/mL">1.125</concentration>
                    <buffer>
                        <ph>7.5</ph>
                        <component>
                            <concentration units="mM">20.0</concentration>
                            <formula>C8H18N2O4S</formula>
                            <name>HEPES</name>
                        </component>
                        <component>
                            <concentration units="mM">50.0</concentration>
                            <formula>NaCl</formula>
                            <name>sodium chloride</name>
                        </component>
                        <component>
                            <concentration units="mM">0.5</concentration>
                            <formula>C10H16N2O8</formula>
                            <name>EDTA</name>
                        </component>
                        <component>
                            <concentration units="mM">4.0</concentration>
                            <formula>MgCl2</formula>
                            <name>magnesium chloride</name>
                        </component>
                    </buffer>
                    <grid>
                        <model>Quantifoil R2/1</model>
                        <material>COPPER</material>
                        <mesh>300</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>HOLEY</film_topology>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                            <time units="s">30</time>
                            <atmosphere>AIR</atmosphere>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">298</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <details>Blot time was 2 sec.. </details>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TITAN KRIOS</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">300</acceleration_voltage>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K3 (6k x 4k)</film_or_detector_model>
                            <number_grids_imaged>1</number_grids_imaged>
                            <number_real_images>2519</number_real_images>
                            <average_exposure_time units="s">0.11984</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">1.552</average_electron_dose_per_image>
                        </image_recording>
                        <image_recording image_recording_id="2">
                            <film_or_detector_model>GATAN K3 (6k x 4k)</film_or_detector_model>
                            <number_grids_imaged>1</number_grids_imaged>
                            <number_real_images>3063</number_real_images>
                            <average_exposure_time units="s">0.12</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">1.55</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>690973</number_selected>
                </particle_selection>
                <startup_model type_of_model="EMDB MAP"/>
                <final_reconstruction>
                    <number_classes_used>1</number_classes_used>
                    <applied_symmetry>
                        <point_group>C2</point_group>
                    </applied_symmetry>
                    <resolution units="Å" res_type="BY AUTHOR">3.45</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>3.0</version>
                        </software>
                    </software_list>
                    <number_images_used>178107</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>3.0</version>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>3.0</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
                <final_three_d_classification>
                    <number_classes>6</number_classes>
                    <average_number_members_per_class>59363.0</average_number_members_per_class>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>3.0</version>
                        </software>
                    </software_list>
                </final_three_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="101649">
        <file>emd_10528.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>294</col>
            <row>294</row>
            <sec>294</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>294</x>
            <y>294</y>
            <z>294</z>
        </spacing>
        <cell>
            <a units="Å">320.46002</a>
            <b units="Å">320.46002</b>
            <c units="Å">320.46002</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>-0.10070717</minimum>
            <maximum>0.18211088</maximum>
            <average>0.0007228104</average>
            <std>0.005765548</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.09</x>
            <y units="Å">1.09</y>
            <z units="Å">1.09</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.025</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-10528::::</label>
        <annotation_details>CryoEM map of apo gp146, the chaperonin from bacteriophage EL (Pseudomonas putida)</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <details>Jelly body refinement
C2 symmetry NCS restraints</details>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
