<emd emdb_id="EMD-5034" 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>2008-11-10</deposition>
            <header_release>2008-11-18</header_release>
            <map_release>2009-04-15</map_release>
            <update>2009-04-15</update>
        </key_dates>
        <title>Structure of a type IV secretion system core complex</title>
        <authors_list>
            <author>Fronzes R</author>
            <author>Schafer E</author>
            <author>Wang L</author>
            <author>Saibil H</author>
            <author>Orlova E</author>
            <author>Waksman G</author>
        </authors_list>
        <keywords>bacterial secretion,type IV secretion,vir,tra</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Fronzes R</author>
                    <author order="2">Schafer E</author>
                    <author order="3">Wang L</author>
                    <author order="4">Saibil HR</author>
                    <author order="5">Orlova EV</author>
                    <author order="6">Waksman G</author>
                    <title>Structure of a type IV secretion system core complex.</title>
                    <journal>SCIENCE</journal>
                    <volume>323</volume>
                    <first_page>266</first_page>
                    <last_page>268</last_page>
                    <year>2009</year>
                    <external_references type="PUBMED">19131631</external_references>
                    <external_references type="DOI">doi:10.1126/science.1166101</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>traN/traO/traF complex encoded by pKM101
Digested with 2mg ml-1 of trypsin for 2 hours at room temperature.</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>traN/traO/traF complex encoded by pKM101
Digested with 2mg ml-1 of trypsin for 2 hours at room temperature.</name>
                <details>monodisperse</details>
                <oligomeric_state>14-mer</oligomeric_state>
                <number_unique_components>3</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">0.602</experimental>
                    <theoretical units="MDa">0.5</theoretical>
                    <method>gel filtration</method>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="traF">traF</name>
                <natural_source database="NCBI">
                    <organism />
                    <strain>BL21</strain>
                    <cell>Escherichia coli</cell>
                    <cellular_location>inner membrane</cellular_location>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.04</theoretical>
                </molecular_weight>
                <number_of_copies>14</number_of_copies>
                <oligomeric_state>14-mer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_plasmid>pASK-IBA3c</recombinant_plasmid>
                </recombinant_expression>
                <sequence />
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name synonym="traO">traO</name>
                <natural_source database="NCBI">
                    <organism />
                    <strain>BL21</strain>
                    <cell>Escherichia coli</cell>
                    <cellular_location>outer membrane</cellular_location>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.03</theoretical>
                </molecular_weight>
                <number_of_copies>14</number_of_copies>
                <oligomeric_state>14-mer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_plasmid>pASK-IBA3c</recombinant_plasmid>
                </recombinant_expression>
                <sequence />
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="3">
                <name synonym="traN">traN</name>
                <natural_source database="NCBI">
                    <organism />
                    <strain>BL21</strain>
                    <cell>Escherichia coli</cell>
                    <cellular_location>outer membrane</cellular_location>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.005</theoretical>
                </molecular_weight>
                <number_of_copies>14</number_of_copies>
                <oligomeric_state>14-mer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_plasmid>pASK-IBA3c</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">5</concentration>
                    <buffer>
                        <ph>8.0</ph>
                        <details>50 mM Tris-HCL, 200 mM NaCl, 10 mM LDAO</details>
                    </buffer>
                    <grid>
                        <details>lacey carbon grids</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">60</chamber_humidity>
                        <chamber_temperature units="K">92</chamber_temperature>
                        <instrument>OTHER</instrument>
                        <method>blot 3 seconds before plunging</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI F20</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_cs units="mm">2.1</nominal_cs>
                    <nominal_defocus_min units="&#181;m">1.25</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">3.5</nominal_defocus_max>
                    <nominal_magnification>66000.0</nominal_magnification>
                    <calibrated_magnification>68100.0</calibrated_magnification>
                    <specimen_holder_model>OTHER</specimen_holder_model>
                    <temperature>
                        <temperature_average units="K">95</temperature_average>
                    </temperature>
                    <details>4000x4000 CCD</details>
                    <date>2008-01-01</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GENERIC GATAN</film_or_detector_model>
                            <digitization_details>
                                <sampling_interval units="&#181;m">15</sampling_interval>
                            </digitization_details>
                            <number_real_images>60</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">20</average_electron_dose_per_image>
                            <bits_per_pixel>8.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Side entry liquid nitrogen-cooled cryo specimen holder</specimen_holder>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <ctf_correction>
                    <details>phase flipping, each CCD image</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>imagic</name>
                        </software>
                    </software_list>
                    <details>final map were calculated from 200 class averages.</details>
                    <number_images_used>1557</number_images_used>
                </final_reconstruction>
                <final_two_d_classification>
                    <number_classes>200</number_classes>
                </final_two_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="16001">
        <file>emd_5034.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>160</col>
            <row>160</row>
            <sec>160</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>160</x>
            <y>160</y>
            <z>160</z>
        </spacing>
        <cell>
            <a units="&#8491;">355.2</a>
            <b units="&#8491;">355.2</b>
            <c units="&#8491;">355.2</c>
            <alpha units="deg">90</alpha>
            <beta units="deg">90</beta>
            <gamma units="deg">90</gamma>
        </cell>
        <axis_order>
            <fast>X</fast>
            <medium>Y</medium>
            <slow>Z</slow>
        </axis_order>
        <statistics>
            <minimum>-0.183967</minimum>
            <maximum>0.239721</maximum>
            <average>0.000159712</average>
            <std>0.0105097</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.22</x>
            <y units="&#8491;">2.22</y>
            <z units="&#8491;">2.22</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.0108</level>
            </contour>
        </contour_list>
        <annotation_details>volume</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5034::::</details>
    </map>
</emd>