<emd emdb_id="EMD-5739" 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>2013-08-09</deposition>
            <header_release>2013-09-11</header_release>
            <map_release>2013-09-11</map_release>
            <update>2013-10-09</update>
        </key_dates>
        <title>Electron microscopy map of the T6SS TssK component</title>
        <authors_list>
            <author>Zoued A</author>
            <author>Durand E</author>
            <author>Bebeacua C</author>
            <author>Brunet YR</author>
            <author>Douzi B</author>
            <author>Cambillau C</author>
            <author>Cascales E</author>
            <author>Journet L</author>
        </authors_list>
        <keywords>TssK, Type VI secretion, Hcp, sheath assembly, EM, single-particle, three-fold</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Zoued A</author>
                    <author order="2">Durand E</author>
                    <author order="3">Bebeacua C</author>
                    <author order="4">Brunet YR</author>
                    <author order="5">Douzi B</author>
                    <author order="6">Cambillau C</author>
                    <author order="7">Cascales E</author>
                    <author order="8">Journet L</author>
                    <title>TssK is a trimeric cytoplasmic protein interacting with components of both phage-like and membrane anchoring complexes of the type VI secretion system.</title>
                    <journal>J.BIOL.CHEM.</journal>
                    <volume>288</volume>
                    <first_page>27031</first_page>
                    <last_page>27041</last_page>
                    <year>2013</year>
                    <external_references type="PUBMED">23921384</external_references>
                    <external_references type="DOI">doi:10.1074/jbc.M113.499772</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Purified TssK sample</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Purified TssK sample</name>
                <details>The sample was monodisperse.</details>
                <oligomeric_state>3</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">0.160</experimental>
                    <method>Analytical size exclusion chromatography analysis</method>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="TssK">Type VI secretion system protein TssK</name>
                <natural_source database="NCBI">
                    <organism ncbi="562">Escherichia coli</organism>
                    <strain>042</strain>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">0.16</experimental>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <oligomeric_state>Trimer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_strain>T7 Iq pLys</recombinant_strain>
                    <recombinant_plasmid>pETG20-TssK1</recombinant_plasmid>
                </recombinant_expression>
                <sequence>
                    <external_references type="UNIPROTKB">Q74G23</external_references>
                    <external_references type="GO">GO:0008150</external_references>
                    <external_references type="GO">GO:0003674</external_references>
                    <external_references type="GO">GO:0005575</external_references>
                    <external_references type="INTERPRO">IPR010263</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">0.05</concentration>
                    <buffer>
                        <ph>8.0</ph>
                        <details>HBS-EP buffer (10mM HEPES, 150mM NaCl, 3mM EDTA, 0.005% Polysorbate 20)</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <details>Purified protein was immobilized on a glow-
discharged carbon grid by incubation for 1
minute, and then stained with 2% uranyl
acetate for 10 seconds.</details>
                    </staining>
                    <grid>
                        <details>300 mesh copper grid with thin carbon support, glow discharged for 20 seconds</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>FEI TECNAI SPIRIT</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>LAB6</electron_source>
                    <acceleration_voltage units="kV">120</acceleration_voltage>
                    <nominal_cs units="mm">2</nominal_cs>
                    <nominal_defocus_min units="&#181;m">2.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">3.0</nominal_defocus_max>
                    <nominal_magnification>60000.0</nominal_magnification>
                    <specimen_holder_model>SIDE ENTRY, EUCENTRIC</specimen_holder_model>
                    <date>2012-11-01</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GENERIC CCD</film_or_detector_model>
                            <number_real_images>10</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">10</average_electron_dose_per_image>
                            <details>CCD images</details>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Room temperature holder</specimen_holder>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>The particles were submitted to maximum likelihood classification and alignment.</details>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">26.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN, SPIDER, XMIPP</name>
                        </software>
                    </software_list>
                    <number_images_used>5000</number_images_used>
                </final_reconstruction>
                <final_angle_assignment>
                    <details>ML</details>
                </final_angle_assignment>
                <final_two_d_classification>
                    <number_classes>500</number_classes>
                </final_two_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="1459">
        <file>emd_5739.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>72</col>
            <row>72</row>
            <sec>72</sec>
        </dimensions>
        <origin>
            <col>-36</col>
            <row>-36</row>
            <sec>-36</sec>
        </origin>
        <spacing>
            <x>72</x>
            <y>72</y>
            <z>72</z>
        </spacing>
        <cell>
            <a units="&#8491;">252.0</a>
            <b units="&#8491;">252.0</b>
            <c units="&#8491;">252.0</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>0.0</minimum>
            <maximum>0.13164011</maximum>
            <average>0.00123267</average>
            <std>0.00891095</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">3.5</x>
            <y units="&#8491;">3.5</y>
            <z units="&#8491;">3.5</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.04</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>EM Reconstruction of TssK</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5739::::</details>
    </map>
    <interpretation>
        <figure_list>
            <figure>
                <file>emd_5739.png</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>