<?xml version="1.0" encoding="UTF-8"?>
<emd emdb_id="EMD-3060" version="3.0.1.9">
    <admin>
        <status_history_list>
            <status status_id="1">
                <code>HPUB</code>
            </status>
        </status_history_list>
        <current_status>
            <code superseded="true">OBS</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2015-06-22</deposition>
            <header_release>2015-08-12</header_release>
            <obsolete>2016-02-10</obsolete>
            <update>2016-02-10</update>
        </key_dates>
        <superseded_by_list>
            <entry>
                <entry>EMD-3233</entry>
            </entry>
        </superseded_by_list>
        <title>Phase plate structure of Peroxiredoxin-3 dodecamers</title>
        <authors_list>
            <author>Khoshouei M</author>
            <author>Radjainia M</author>
            <author>Abrishami V</author>
            <author>Phillips AJ</author>
            <author>Gerrard JA</author>
            <author>Mitra AK</author>
            <author>Plitzko JM</author>
            <author>Baumeister W</author>
            <author>Danev R</author>
        </authors_list>
        <keywords>Volta phase plate, peroxiredoxin, peroxidase, antioxidant</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="false">
                    <author order="1">Khoshouei M</author>
                    <author order="2">Radjainia M</author>
                    <author order="3">Abrishami V</author>
                    <author order="4">Phillips AJ</author>
                    <author order="5">Gerrard JA</author>
                    <author order="6">Mitra AK</author>
                    <author order="7">Plitzko JM</author>
                    <author order="8">Baumeister W</author>
                    <author order="9">Danev R</author>
                    <title>Volta phase plate cryo-EM of the small protein complex Prx3</title>
                    <journal>NAT.COMMUN.</journal>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Peroxiredoxin-3 dodecamers</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Peroxiredoxin-3 dodecamers</name>
                <details>The sample was monodisperse</details>
                <oligomeric_state>12</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">0.257</experimental>
                    <theoretical units="MDa">0.257</theoretical>
                    <method>SEC and MS</method>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="Prx3">Human Peroxiredoxin-3</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>Human</synonym_organism>
                    <organelle>Mitochondria</organelle>
                    <cellular_location>matrix</cellular_location>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">0.257</experimental>
                    <theoretical units="MDa">0.257</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <oligomeric_state>dodecamer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <sequence>
                    <external_references type="UNIPROTKB">P30048</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">1</concentration>
                    <buffer>
                        <ph>8.0</ph>
                        <details>20mM Hepes pH8, 150m NaCl</details>
                    </buffer>
                    <grid>
                        <details>Quantifoil R2/2</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <instrument>FEI VITROBOT MARK III</instrument>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TITAN KRIOS</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>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <date>2015-02-26</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN K2 (4k x 4k)</film_or_detector_model>
                            <number_real_images>44</number_real_images>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <final_reconstruction>
                    <resolution units="Å" res_type="BY AUTHOR">7.3</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>Relion</name>
                        </software>
                    </software_list>
                    <number_images_used>7000</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="13719">
        <file>emd_3060.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>152</col>
            <row>152</row>
            <sec>152</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>152</x>
            <y>152</y>
            <z>152</z>
        </spacing>
        <cell>
            <a units="Å">205.2</a>
            <b units="Å">205.2</b>
            <c units="Å">205.2</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>-0.07650846</minimum>
            <maximum>0.11458807</maximum>
            <average>0.00075023</average>
            <std>0.0070431</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.35</x>
            <y units="Å">1.35</y>
            <z units="Å">1.35</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.024</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Single-particle reconstruction of Prx3 dodecamers from Volta Phase Contrast Images</annotation_details>
        <details>::::EMDATABANK.org::::EMD-3060::::</details>
    </map>
    <validation>
        <fsc_curve>
            <file>emd_3060_fsc.xml</file>
        </fsc_curve>
    </validation>
</emd>
