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    <admin>
        <current_status>
            <date>2024-05-29</date>
            <code>REL</code>
            <processing_site>PDBj</processing_site>
        </current_status>
        <sites>
            <deposition>PDBj</deposition>
            <last_processing>PDBj</last_processing>
        </sites>
        <key_dates>
            <deposition>2019-08-05</deposition>
            <header_release>2020-08-12</header_release>
            <map_release>2020-08-12</map_release>
            <update>2024-05-29</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Japan Agency for Medical Research and Development (AMED)</funding_body>
                <code>JP19am0101071</code>
                <country>Japan</country>
            </grant_reference>
        </grant_support>
        <title>CryoEM map and model of Nitrite Reductase at pH 8.1</title>
        <authors_list>
            <author>Adachi N</author>
            <author>Yamaguchi T</author>
            <author>Moriya T</author>
            <author>Kawasaki M</author>
            <author>Koiwai K</author>
            <author>Shinoda A</author>
            <author>Yamada Y</author>
            <author>Yumoto F</author>
            <author>Kohzuma T</author>
            <author>Senda T</author>
        </authors_list>
        <keywords>Cu containing nitrite reductase, OXIDOREDUCTASE</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Adachi N</author>
                    <author order="2">Yamaguchi T</author>
                    <author order="3">Moriya T</author>
                    <author order="4">Kawasaki M</author>
                    <author order="5">Koiwai K</author>
                    <author order="6">Shinoda A</author>
                    <author order="7">Yamada Y</author>
                    <author order="8">Yumoto F</author>
                    <author order="9">Kohzuma T</author>
                    <author order="10">Senda T</author>
                    <title>2.85 and 2.99 angstrom resolution structures of 110 kDa nitrite reductase determined by 200 kV cryogenic electron microscopy.</title>
                    <journal_abbreviation>J.Struct.Biol.</journal_abbreviation>
                    <country>US</country>
                    <volume>213</volume>
                    <first_page>107768</first_page>
                    <last_page>107768</last_page>
                    <year>2021</year>
                    <external_references type="PUBMED">34217801</external_references>
                    <external_references type="DOI">doi:10.1016/j.jsb.2021.107768</external_references>
                    <external_references type="ISSN">1095-8657</external_references>
                    <external_references type="CSD">0803</external_references>
                    <external_references type="ASTM">JSBIEM</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>6kng</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Nitrite reductase</name>
        <supramolecule_list>
            <organelle_or_cellular_component_supramolecule supramolecule_id="1">
                <name>Nitrite reductase</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="223">Achromobacter cycloclastes</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.11</theoretical>
                </molecular_weight>
            </organelle_or_cellular_component_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Copper-containing nitrite reductase</name>
                <natural_source database="NCBI">
                    <organism ncbi="223">Achromobacter cycloclastes</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.036621332</theoretical>
                </molecular_weight>
                <number_of_copies>3</number_of_copies>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>VDISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLI
NPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEK
GQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHS
QANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGEW
NDDLMTSVVKPASM</string>
                    <external_references type="UNIPROTKB">P25006</external_references>
                </sequence>
                <ec_number>1.7.2.1</ec_number>
            </protein_or_peptide>
            <ligand macromolecule_id="2">
                <name>COPPER (II) ION</name>
                <molecular_weight>
                    <theoretical units="MDa">6.354599999999999e-05</theoretical>
                </molecular_weight>
                <number_of_copies>6</number_of_copies>
                <formula>CU</formula>
            </ligand>
        </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">1.1</concentration>
                    <buffer>
                        <ph>8.1</ph>
                        <component>
                            <concentration units="mM">100.0</concentration>
                            <name>pottasium phosphate</name>
                        </component>
                    </buffer>
                    <grid>
                        <model>Quantifoil R1.2/1.3</model>
                        <material>COPPER</material>
                        <mesh>300</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>HOLEY</film_topology>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                            <time units="s">30</time>
                            <atmosphere>AIR</atmosphere>
                        </pretreatment>
                        <details>The grid was washed by acetone prior to use.</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">291</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <details>Blotting time was 15 seconds.. </details>
                    </vitrification>
                    <details>This sample was mono-disperse.</details>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TALOS ARCTICA</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>
                    <c2_aperture_diameter units="µm">50.0</c2_aperture_diameter>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="µm">1.0</nominal_defocus_min>
                    <nominal_defocus_max units="µm">3.0</nominal_defocus_max>
                    <nominal_magnification>120000.0</nominal_magnification>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>FEI FALCON III (4k x 4k)</film_or_detector_model>
                            <detector_mode>COUNTING</detector_mode>
                            <number_grids_imaged>1</number_grids_imaged>
                            <number_real_images>694</number_real_images>
                            <average_exposure_time units="s">56.37</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">50.0</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <startup_model type_of_model="OTHER">
                    <details>An ab initio model was generated using RELION3's own implementation of Stochastic Gradient Descent (SGD) algorithm and low-pass filtered to 25 A for use as an initial model for 3D refinement.</details>
                </startup_model>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>C3</point_group>
                    </applied_symmetry>
                    <resolution units="Å" res_type="BY AUTHOR">2.85</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>3</version>
                        </software>
                    </software_list>
                    <number_images_used>89513</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>3</version>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>3</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="459166">
        <file>emd_0731.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>486</col>
            <row>486</row>
            <sec>486</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>486</x>
            <y>486</y>
            <z>486</z>
        </spacing>
        <cell>
            <a units="Å">427.68</a>
            <b units="Å">427.68</b>
            <c units="Å">427.68</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>-0.07121556</minimum>
            <maximum>0.16267285</maximum>
            <average>-0.0000037978973</average>
            <std>0.0022694988</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">0.88</x>
            <y units="Å">0.88</y>
            <z units="Å">0.88</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.0405</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-0731::::</label>
    </map>
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