<emd emdb_id="EMD-2328" 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>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2013-03-10</deposition>
            <header_release>2013-03-20</header_release>
            <map_release>2013-04-17</map_release>
            <update>2013-08-28</update>
        </key_dates>
        <title>Structure of the bacterial V-ATPase from Thermus thermophilius</title>
        <authors_list>
            <author>Tani K</author>
            <author>Arthur CP</author>
            <author>Tamakoshi M</author>
            <author>Yokoyama K</author>
            <author>Mitsuoka K</author>
            <author>Fujiyoshi Y</author>
            <author>Gerle C</author>
        </authors_list>
        <keywords>bacterial V-ATPase, rotary ATPase</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Tani K</author>
                    <author order="2">Arthur CP</author>
                    <author order="3">Tamakoshi M</author>
                    <author order="4">Yokoyama K</author>
                    <author order="5">Mitsuoka K</author>
                    <author order="6">Fujiyoshi Y</author>
                    <author order="7">Gerle C</author>
                    <title>Visualization of two distinct states of disassembly in the bacterial V-ATPase from Thermus thermophilus.</title>
                    <journal>Microscopy</journal>
                    <volume>62</volume>
                    <first_page>467</first_page>
                    <last_page>474</last_page>
                    <year>2013</year>
                    <external_references type="PUBMED">23572213</external_references>
                    <external_references type="DOI">doi:10.1093/jmicro/dft020</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Bacterial V-type ATPase</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Bacterial V-type ATPase</name>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>V-ATPase</name>
                <natural_source database="NCBI">
                    <organism ncbi="274">Thermus thermophilus</organism>
                    <cellular_location>Plasma membrane</cellular_location>
                </natural_source>
                <number_of_copies>2</number_of_copies>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <sequence />
            </protein_or_peptide>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>electronCrystallography</method>
            <aggregation_state>twoDArray</aggregation_state>
            <specimen_preparation_list>
                <crystallography_preparation preparation_id="1">
                    <concentration units="mg/mL">1</concentration>
                    <staining>
                        <type>NEGATIVE</type>
                        <details>A 2.5 ul sample was transferred to a glow-discharged carbon coated copper grid. After 1 min, the drop was blotted with a slice of filter paper, and then the grid was washed with 2.5 ul water to avoid the precipitation caused by mixing phosphate buffer with uranyl acetate. Subsequently, the sample was stained with 2.5 ul of 2% uranyl acetate and air-dried.</details>
                    </staining>
                    <grid>
                        <details>a glow-discharged carbon coated copper grid</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>NONE</cryogen_name>
                        <instrument>OTHER</instrument>
                    </vitrification>
                    <details>Crystals grown by dialysis</details>
                    <crystal_formation>
                        <details>Crystals grown by dialysis</details>
                    </crystal_formation>
                </crystallography_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <crystallography_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI F30</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_defocus_min units="&#181;m">1.4</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">2.27</nominal_defocus_max>
                    <nominal_magnification>40000.0</nominal_magnification>
                    <specimen_holder_model>SIDE ENTRY, EUCENTRIC</specimen_holder_model>
                    <date>2007-11-28</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>212</number_real_images>
                            <details>Every image was recorded by 2Kx2K CCD camera (Gatan)</details>
                            <bits_per_pixel>16.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                    <tilt_angle_min>-55</tilt_angle_min>
                    <tilt_angle_max>55</tilt_angle_max>
                    <tilt_series>
                        <axis1>
                            <min_angle units="deg">-55</min_angle>
                            <max_angle units="deg">55</max_angle>
                        </axis1>
                    </tilt_series>
                </crystallography_microscopy>
            </microscopy_list>
            <crystallography_processing image_processing_id="1">
                <details>Images were processed using MRC package</details>
                <final_reconstruction>
                    <resolution res_type="BY AUTHOR" units="&#8491;">18.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>MRC</name>
                        </software>
                    </software_list>
                </final_reconstruction>
                <crystal_parameters>
                    <unit_cell>
                        <a units="&#8491;">232</a>
                        <b units="&#8491;">132</b>
                        <c units="&#8491;">300</c>
                        <gamma units="deg">90.0</gamma>
                        <alpha units="deg">90.0</alpha>
                        <beta units="deg">90.0</beta>
                    </unit_cell>
                    <plane_group>P 1</plane_group>
                </crystal_parameters>
            </crystallography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="488">
        <file>emd_2328.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>31</col>
            <row>55</row>
            <sec>73</sec>
        </dimensions>
        <origin>
            <col>-15</col>
            <row>-27</row>
            <sec>-36</sec>
        </origin>
        <spacing>
            <x>30</x>
            <y>54</y>
            <z>72</z>
        </spacing>
        <cell>
            <a units="&#8491;">231.984</a>
            <b units="&#8491;">132.0</b>
            <c units="&#8491;">299.952</c>
            <alpha units="deg">90.0</alpha>
            <beta units="deg">90.0</beta>
            <gamma units="deg">90.0</gamma>
        </cell>
        <axis_order>
            <fast>Y</fast>
            <medium>X</medium>
            <slow>Z</slow>
        </axis_order>
        <statistics>
            <minimum>-3.48900008</minimum>
            <maximum>6.74800014</maximum>
            <average>-0.00587434</average>
            <std>0.98739201</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">4.296</x>
            <y units="&#8491;">4.4</y>
            <z units="&#8491;">4.166</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.4</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of the bacterial V-ATPase</annotation_details>
        <details>::::EMDATABANK.org::::EMD-2328::::</details>
    </map>
</emd>