<emd emdb_id="EMD-5505" 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>2012-09-28</deposition>
            <header_release>2012-10-10</header_release>
            <map_release>2012-10-24</map_release>
            <update>2012-11-28</update>
        </key_dates>
        <title>Hexameric structure of the conjugative VirB4 ATPase TrwK: new insights into a functional and phylogenetic relationship with DNA translocases</title>
        <authors_list>
            <author>Pena A</author>
            <author>Matilla I</author>
            <author>Martin-Benito J</author>
            <author>Valpuesta JM</author>
            <author>Carrascosa JL</author>
            <author>De la Cruz F</author>
            <author>Cabezon E</author>
            <author>Arechaga I</author>
        </authors_list>
        <keywords>bacterial secretion systems, conjugation</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Pena A</author>
                    <author order="2">Matilla I</author>
                    <author order="3">Martin-Benito J</author>
                    <author order="4">Valpuesta JM</author>
                    <author order="5">Carrascosa JL</author>
                    <author order="6">De la Cruz F</author>
                    <author order="7">Cabezon E</author>
                    <author order="8">Arechaga I</author>
                    <title>The hexameric structure of a conjugative VirB4 protein ATPase provides new insights for a functional and phylogenetic relationship with DNA translocases.</title>
                    <journal>J.BIOL.CHEM.</journal>
                    <volume>287</volume>
                    <first_page>39925</first_page>
                    <last_page>39932</last_page>
                    <year>2012</year>
                    <external_references type="PUBMED">23035111</external_references>
                    <external_references type="DOI">doi:10.1074/jbc.M112.413849</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Hexameric TrwK</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Hexameric TrwK</name>
                <oligomeric_state>hexameric</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">0.54</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="VirB4">VirB4 component of type IV transporter system</name>
                <natural_source database="NCBI">
                    <organism ncbi="562">Escherichia coli</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.54</theoretical>
                </molecular_weight>
                <oligomeric_state>Hexamer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_plasmid>pET</recombinant_plasmid>
                </recombinant_expression>
                <sequence>
                    <external_references type="GO">GO:0005524</external_references>
                    <external_references type="INTERPRO">IPR004346</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">0.1</concentration>
                    <buffer>
                        <ph>6.45</ph>
                        <details>50 mM PIPES-NaOH, 75 mM potassium acetate, 5% (w/v) glycerol, 10 mM magnesium acetate, 0.1 mM EDTA, and 0.5 mM phenylmethylsulfonyl fluoride.</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <details>Samples were negatively stained with 2% (w/v) uranyl acetate</details>
                    </staining>
                    <grid>
                        <details>freshly glow-discharged carbon-coated grids</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>NONE</cryogen_name>
                        <instrument>OTHER</instrument>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>JEOL 1200EXII</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>TUNGSTEN HAIRPIN</electron_source>
                    <acceleration_voltage units="kV">100</acceleration_voltage>
                    <nominal_cs units="mm">5.6</nominal_cs>
                    <nominal_defocus_min units="&#181;m">0.6</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">1.0</nominal_defocus_max>
                    <nominal_magnification>60000.0</nominal_magnification>
                    <specimen_holder_model>JEOL</specimen_holder_model>
                    <date>2011-12-11</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="FILM">KODAK SO-163 FILM</film_or_detector_model>
                            <digitization_details>
                                <scanner>ZEISS SCAI</scanner>
                            </digitization_details>
                            <average_electron_dose_per_image units="e/&#8491;^2">20</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <ctf_correction>
                    <details>Yes</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">20.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>XMIPP</name>
                        </software>
                    </software_list>
                    <number_images_used>1179</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="617">
        <file>emd_5505.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>54</col>
            <row>54</row>
            <sec>54</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>54</x>
            <y>54</y>
            <z>54</z>
        </spacing>
        <cell>
            <a units="&#8491;">251.63998</a>
            <b units="&#8491;">251.63998</b>
            <c units="&#8491;">251.63998</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>-0.07715909</minimum>
            <maximum>0.11468405</maximum>
            <average>0.00622329</average>
            <std>0.02549224</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">4.66</x>
            <y units="&#8491;">4.66</y>
            <z units="&#8491;">4.66</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.05</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of hexameric TrwK</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5505::::</details>
    </map>
    <interpretation>
        <figure_list>
            <figure>
                <file>emd_5505.tif</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>