<emd emdb_id="EMD-2068" 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>2012-04-06</deposition>
            <header_release>2012-04-13</header_release>
            <map_release>2012-05-17</map_release>
            <update>2016-04-20</update>
        </key_dates>
        <title>Alp12 filament structure</title>
        <authors_list>
            <author>Popp D</author>
            <author>Narita A</author>
            <author>Lee LJ</author>
            <author>Ghoshdastider U</author>
            <author>Xue B</author>
            <author>Srinivasan R</author>
            <author>Balasubramanian MK</author>
            <author>Tanaka T</author>
            <author>Robinson RC</author>
        </authors_list>
        <keywords>Alp12, actin-like protein, Clostridium tetani</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Popp D</author>
                    <author order="2">Narita A</author>
                    <author order="3">Lee LJ</author>
                    <author order="4">Ghoshdastider U</author>
                    <author order="5">Xue B</author>
                    <author order="6">Srinivasan R</author>
                    <author order="7">Balasubramanian MK</author>
                    <author order="8">Tanaka T</author>
                    <author order="9">Robinson RC</author>
                    <title>Novel actin-like filament structure from Clostridium tetani.</title>
                    <journal>J.BIOL.CHEM.</journal>
                    <volume>287</volume>
                    <first_page>21121</first_page>
                    <last_page>21129</last_page>
                    <year>2012</year>
                    <external_references type="PUBMED">22514279</external_references>
                    <external_references type="DOI">doi:10.1074/jbc.M112.341016</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>4apw</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Filament structure of an actin-like protein, Alp12, in Clostridium tetani</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Filament structure of an actin-like protein, Alp12, in Clostridium tetani</name>
                <oligomeric_state>Helical filament</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <method>Sequence</method>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Alp12</name>
                <natural_source database="NCBI">
                    <organism ncbi="1513">Clostridium tetani</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.037</theoretical>
                </molecular_weight>
                <oligomeric_state>Filament</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="469008">Escherichia coli BL21(DE3)</recombinant_organism>
                    <recombinant_plasmid>pSY5</recombinant_plasmid>
                </recombinant_expression>
                <sequence />
            </protein_or_peptide>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>helical</method>
            <aggregation_state>filament</aggregation_state>
            <specimen_preparation_list>
                <helical_preparation preparation_id="1">
                    <concentration units="mg/mL">0.35</concentration>
                    <buffer>
                        <ph>7.5</ph>
                        <details>300 mM KCl, 1 mM MgCl2, 0.5 mM DTT, 30 mM Hepes, 1 mM ATP</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <details>A drop of Alp12 solution was applied to grids, blotted, stained with 1 % uranyl acetate</details>
                    </staining>
                    <grid>
                        <details>200 mesh copper grid with thin carbon support</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>NONE</cryogen_name>
                        <instrument>OTHER</instrument>
                        <method>Negatively staining</method>
                    </vitrification>
                </helical_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <helical_microscopy microscopy_id="1">
                    <microscope>HITACHI H7600</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>LAB6</electron_source>
                    <acceleration_voltage units="kV">100</acceleration_voltage>
                    <nominal_defocus_min units="&#181;m">0.8</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">5.0</nominal_defocus_max>
                    <nominal_magnification>40000.0</nominal_magnification>
                    <specimen_holder_model>SIDE ENTRY, EUCENTRIC</specimen_holder_model>
                    <date>2011-09-06</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>
                                <sampling_interval units="&#181;m">7</sampling_interval>
                            </digitization_details>
                            <number_real_images>31</number_real_images>
                            <bits_per_pixel>12.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                </helical_microscopy>
            </microscopy_list>
            <helical_processing image_processing_id="1">
                <details>The particles were aligned using Eos.</details>
                <final_reconstruction>
                    <applied_symmetry>
                        <helical_parameters>
                            <delta_z units="&#8491;">42.88</delta_z>
                            <delta_phi units="deg">13.24</delta_phi>
                            <axial_symmetry>D1</axial_symmetry>
                        </helical_parameters>
                    </applied_symmetry>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">19.7</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>EOS</name>
                        </software>
                    </software_list>
                </final_reconstruction>
                <ctf_correction>
                    <details>Each scanned image</details>
                </ctf_correction>
            </helical_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="3126">
        <file>emd_2068.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>100</col>
            <row>100</row>
            <sec>80</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>100</x>
            <y>100</y>
            <z>80</z>
        </spacing>
        <cell>
            <a units="&#8491;">268.0</a>
            <b units="&#8491;">268.0</b>
            <c units="&#8491;">214.40001</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>-1.63097715</minimum>
            <maximum>2.22191262</maximum>
            <average>0.07950152</average>
            <std>0.35939419</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.68</x>
            <y units="&#8491;">2.68</y>
            <z units="&#8491;">2.68</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.88</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of the Alp12 filament</annotation_details>
        <details>::::EMDATABANK.org::::EMD-2068::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>3JS6</access_code>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <details>Protocol: X-RAY</details>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>