<emd emdb_id="EMD-5391" 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>2012-02-07</deposition>
            <header_release>2012-02-16</header_release>
            <map_release>2013-08-07</map_release>
            <update>2013-08-07</update>
        </key_dates>
        <title>8-fold symmetric rATcpn-alpha in apo state</title>
        <authors_list>
            <author>Zhang K</author>
            <author>Wang L</author>
            <author>Liu YX</author>
            <author>Wang X</author>
            <author>Gao B</author>
            <author>Hu ZJ</author>
            <author>Ji G</author>
            <author>Chan KY</author>
            <author>Schulten K</author>
            <author>Dong ZY</author>
            <author>Sun F</author>
        </authors_list>
        <keywords>Group II chaperonin, thermosome</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Zhang K</author>
                    <author order="2">Wang L</author>
                    <author order="3">Liu Y</author>
                    <author order="4">Chan KY</author>
                    <author order="5">Pang X</author>
                    <author order="6">Schulten K</author>
                    <author order="7">Dong Z</author>
                    <author order="8">Sun F</author>
                    <title>Flexible interwoven termini determine the thermal stability of thermosomes.</title>
                    <journal>PROTEIN CELL</journal>
                    <volume>4</volume>
                    <first_page>432</first_page>
                    <last_page>444</last_page>
                    <year>2013</year>
                    <external_references type="PUBMED">23709365</external_references>
                    <external_references type="DOI">doi:10.1007/s13238-013-3026-9</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>3j1b</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>rATcpn-alpha in apo state</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>rATcpn-alpha in apo state</name>
                <details>This sample contains about 90% 8-fold symmetric particles and about 10% 9-fold symmetric particles</details>
                <oligomeric_state>hexadecamer</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">0.96</experimental>
                    <theoretical units="MDa">0.96</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="rATcpn-alpha">Group II chaperonin alpha</name>
                <natural_source database="NCBI">
                    <organism ncbi="146920">Acidianus tengchongensis</organism>
                    <strain>S5T</strain>
                    <synonym_organism>Archaea</synonym_organism>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">0.96</experimental>
                    <theoretical units="MDa">0.96</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <oligomeric_state>hexadecamer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_plasmid>PET-23b</recombinant_plasmid>
                </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">
                    <concentration units="mg/mL">3</concentration>
                    <buffer>
                        <ph>7.5</ph>
                        <details>25 mM Tris-HCl, pH 7.5, 12 mM MgCl2, 50 mM KCl</details>
                    </buffer>
                    <grid>
                        <details>400-mesh GiGTM grid with holes of 2 um diameter and 2 um spacing</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">100</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <method>Blot for 4 seconds before plunging</method>
                    </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>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="&#181;m">1.5</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">3.5</nominal_defocus_max>
                    <nominal_magnification>96000.0</nominal_magnification>
                    <calibrated_magnification>96000.0</calibrated_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>Objective lens astigmatism was corrected at 96,000 times magnification</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <date>2010-07-23</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN ULTRASCAN 4000 (4k x 4k)</film_or_detector_model>
                            <number_real_images>3424</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">20</average_electron_dose_per_image>
                            <bits_per_pixel>32.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <ctf_correction>
                    <details>The whole micrograph</details>
                </ctf_correction>
                <final_reconstruction>
                    <resolution res_type="BY AUTHOR" units="&#8491;">4.9</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>Spider,EMAN1.9</name>
                        </software>
                    </software_list>
                    <number_images_used>55460</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="93313">
        <file>emd_5391.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>288</col>
            <row>288</row>
            <sec>288</sec>
        </dimensions>
        <origin>
            <col>-144</col>
            <row>-144</row>
            <sec>-144</sec>
        </origin>
        <spacing>
            <x>288</x>
            <y>288</y>
            <z>288</z>
        </spacing>
        <cell>
            <a units="&#8491;">268.704</a>
            <b units="&#8491;">268.704</b>
            <c units="&#8491;">268.704</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>-7.62247181</minimum>
            <maximum>13.752257350000001</maximum>
            <average>0.0</average>
            <std>1.2475096</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">0.933</x>
            <y units="&#8491;">0.933</y>
            <z units="&#8491;">0.933</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>3.3</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of the 8-fold symmetric class of apo rATcpn-alpha</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5391::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>3KO1</access_code>
                    <chain>
                        <chain_id>A</chain_id>
                    </chain>
                </initial_model>
                <refinement_protocol>FLEXIBLE FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>Chimera</name>
                    </software>
                </software_list>
                <details>Protocol: Rigid body and Molecular Dynamics Flexible Fitting. symmetry-restrained MDFF</details>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>