<emd emdb_id="EMD-6412" 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>2015-08-02</deposition>
            <header_release>2015-08-12</header_release>
            <map_release>2015-08-12</map_release>
            <update>2015-08-12</update>
        </key_dates>
        <title>Structure of PhnGI complex from Escherichia coli by negative stain</title>
        <authors_list>
            <author>Yang K</author>
            <author>Ren Z</author>
            <author>Raushel FM</author>
            <author>Zhang J</author>
        </authors_list>
        <keywords>PhnGI</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="false">
                    <author order="1">Yang K</author>
                    <author order="2">Ren Z</author>
                    <author order="3">Raushel FM</author>
                    <author order="4">Zhang J</author>
                    <title>Architecture of the Carbon-Phosphorus Lyase Complex from Escherichia coli</title>
                    <journal>To Be Published</journal>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>PhnGI complex from Escherichia coli</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>PhnGI complex from Escherichia coli</name>
                <oligomeric_state>Two PhnG, two PhnI</oligomeric_state>
                <number_unique_components>2</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">0.115</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>PhnG</name>
                <natural_source database="NCBI">
                    <organism ncbi="562">Escherichia coli</organism>
                    <strain>BW5328</strain>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.0187</theoretical>
                </molecular_weight>
                <number_of_copies>2</number_of_copies>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_strain>Rosetta2 (DE3) pLysS cells (Novagen)</recombinant_strain>
                    <recombinant_plasmid>pET-28b</recombinant_plasmid>
                </recombinant_expression>
                <sequence />
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>PhnI</name>
                <natural_source database="NCBI">
                    <organism ncbi="562">Escherichia coli</organism>
                    <strain>BW5328</strain>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.0389</theoretical>
                </molecular_weight>
                <number_of_copies>2</number_of_copies>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_strain>Rosetta2 (DE3) pLysS cells (Novagen)</recombinant_strain>
                    <recombinant_plasmid>pET-28b</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">0.01</concentration>
                    <buffer>
                        <ph>8.5</ph>
                        <details>50 mM HEPES, 150 mM NaCl, 2 mM TCEP</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <details>sample was stained by 2% uranyl acetate</details>
                    </staining>
                    <grid>
                        <details>200 mesh copper grid with carbon film</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>NONE</cryogen_name>
                        <instrument>OTHER</instrument>
                    </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</nominal_cs>
                    <nominal_defocus_min units="&#181;m">3.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">4.1</nominal_defocus_max>
                    <nominal_magnification>40000.0</nominal_magnification>
                    <calibrated_magnification>26285.0</calibrated_magnification>
                    <specimen_holder_model>SIDE ENTRY, EUCENTRIC</specimen_holder_model>
                    <date>2014-05-21</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN ULTRASCAN 1000 (2k x 2k)</film_or_detector_model>
                            <number_real_images>20</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">40</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>Particles were selected in EMAN2. Classification and refinement were performed in Relion.</details>
                <ctf_correction>
                    <details>Each micrograph</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">23.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>CTFFIND4, EMAN2, Relion</name>
                        </software>
                    </software_list>
                    <number_images_used>2298</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="107">
        <file>emd_6412.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>30</col>
            <row>30</row>
            <sec>30</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>30</x>
            <y>30</y>
            <z>30</z>
        </spacing>
        <cell>
            <a units="&#8491;">159.0</a>
            <b units="&#8491;">159.0</b>
            <c units="&#8491;">159.0</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>-0.03472968</minimum>
            <maximum>0.94091636</maximum>
            <average>0.06531542</average>
            <std>0.17226292</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">5.3</x>
            <y units="&#8491;">5.3</y>
            <z units="&#8491;">5.3</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.5</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>PhnGI complex from Escherichia coli</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6412::::</details>
    </map>
    <interpretation>
        <figure_list>
            <figure>
                <file>emd_6412.png</file>
            </figure>
        </figure_list>
    </interpretation>
    <validation>
        <fsc_curve>
            <file>emd_6412_fsc.xml</file>
        </fsc_curve>
    </validation>
</emd>