<emd emdb_id="EMD-5341" 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>2011-09-06</deposition>
            <header_release>2011-11-28</header_release>
            <map_release>2012-08-01</map_release>
            <update>2012-08-01</update>
        </key_dates>
        <title>Chemically controlled assembly of 1, 2 and 3-dimensional protein arrays</title>
        <authors_list>
            <author>Brodin JD</author>
            <author>Ambroggio XI</author>
            <author>Tang C</author>
            <author>Parent KN</author>
            <author>Baker TS</author>
            <author>Tezcan FA</author>
        </authors_list>
        <keywords>nanotube, self assembly, protein array, ridc3, metal coordination</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Brodin JD</author>
                    <author order="2">Ambroggio XI</author>
                    <author order="3">Tang C</author>
                    <author order="4">Parent KN</author>
                    <author order="5">Baker TS</author>
                    <author order="6">Tezcan FA</author>
                    <title>Metal-directed, chemically tunable assembly of one-, two- and three-dimensional crystalline protein arrays.</title>
                    <journal>NAT.CHEM.</journal>
                    <volume>4</volume>
                    <first_page>375</first_page>
                    <last_page>382</last_page>
                    <year>2012</year>
                    <external_references type="PUBMED">22522257</external_references>
                    <external_references type="DOI">doi:10.1038/nchem.1290</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>an engineered cytochrome cb562, RIDC3</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>an engineered cytochrome cb562, RIDC3</name>
                <oligomeric_state>The asymmetric unit is a tetramer</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">0.124</experimental>
                    <method>MALDI</method>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="ridc3">cytochrome cb562 variant</name>
                <natural_source database="NCBI">
                    <organism ncbi="562">Escherichia coli</organism>
                    <synonym_organism>Escherichia coli</synonym_organism>
                    <cellular_location>periplasm</cellular_location>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">0.124</experimental>
                    <theoretical units="MDa">0.124</theoretical>
                </molecular_weight>
                <oligomeric_state>dimer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </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">1.2</concentration>
                    <buffer>
                        <ph>5.5</ph>
                        <details>20 mM MES, 10 mM ZnCl2</details>
                    </buffer>
                    <grid>
                        <details>home-made lacey carbon with a thin layer of continuous carbon</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">89</chamber_temperature>
                        <instrument>HOMEMADE PLUNGER</instrument>
                        <details>Vitrification instrument: manual plunge-freezer</details>
                        <method>Blot for 5 seconds before freezing</method>
                    </vitrification>
                </helical_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <helical_microscopy microscopy_id="1">
                    <microscope>FEI POLARA 300</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">2.3</nominal_cs>
                    <nominal_defocus_min units="&#181;m">1.75</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">3.675</nominal_defocus_max>
                    <nominal_magnification>39000.0</nominal_magnification>
                    <calibrated_magnification>52027.0</calibrated_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">90</temperature_min>
                        <temperature_max units="K">90</temperature_max>
                        <temperature_average units="K">90</temperature_average>
                    </temperature>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>at working magnification</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <date>2011-06-23</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GENERIC GATAN (4k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/&#8491;^2">15</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Polara Multi Specimen Holder</specimen_holder>
                </helical_microscopy>
            </microscopy_list>
            <helical_processing image_processing_id="1">
                <final_reconstruction>
                    <applied_symmetry>
                        <helical_parameters>
                            <delta_z units="&#8491;">25.7</delta_z>
                            <delta_phi units="deg">5.3</delta_phi>
                            <axial_symmetry>C9</axial_symmetry>
                        </helical_parameters>
                    </applied_symmetry>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">10.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>IHRSR</name>
                        </software>
                    </software_list>
                </final_reconstruction>
                <ctf_correction>
                    <details>ROBEM and IHRSR</details>
                </ctf_correction>
            </helical_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="250001">
        <file>emd_5341.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>400</col>
            <row>400</row>
            <sec>400</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>400</x>
            <y>400</y>
            <z>400</z>
        </spacing>
        <cell>
            <a units="&#8491;">1152.0</a>
            <b units="&#8491;">1152.0</b>
            <c units="&#8491;">1152.0</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>-0.4174749</minimum>
            <maximum>0.8219921</maximum>
            <average>0.00576641</average>
            <std>0.08015936</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.88</x>
            <y units="&#8491;">2.88</y>
            <z units="&#8491;">2.88</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.154</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>This is a surface rendered side-view of an engineered RIDC3 nanotube</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5341::::</details>
    </map>
</emd>