<emd emdb_id="EMD-6430" 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>2015-08-20</deposition>
            <header_release>2015-09-23</header_release>
            <map_release>2015-11-11</map_release>
            <update>2016-02-17</update>
        </key_dates>
        <title>Characterization of red-shifted phycobiliprotein complexes isolated from the chlorophyll f-containing cyanobacterium Halomicronema hongdechloris</title>
        <authors_list>
            <author>Li Y</author>
            <author>Lin Y</author>
            <author>Garvey C</author>
            <author>Birch D</author>
            <author>Corkery RW</author>
            <author>Loughlin PC</author>
            <author>Scheer H</author>
            <author>Willows RD</author>
            <author>Chen M</author>
        </authors_list>
        <keywords>phycobiliprotein, complementary chromatic acclimation, far-red light, small angle neutron scattering, photosynthesis, cyanobacteria</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Li Y</author>
                    <author order="2">Lin Y</author>
                    <author order="3">Garvey C</author>
                    <author order="4">Birch D</author>
                    <author order="5">Corkery RW</author>
                    <author order="6">Loughlin PC</author>
                    <author order="7">Scheer H</author>
                    <author order="8">Willows RD</author>
                    <author order="9">Chen M</author>
                    <title>Characterization of red-shifted phycobiliprotein complexes isolated from the chlorophyll f-containing cyanobacterium Halomicronema hongdechloris</title>
                    <journal>Biochim Biophys Acta</journal>
                    <volume>1857</volume>
                    <first_page>107</first_page>
                    <last_page>114</last_page>
                    <year>2016</year>
                    <external_references type="PUBMED">26514405</external_references>
                    <external_references type="DOI">doi:10.1016/j.bbabio.2015.10.009</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>3jbb</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Red-shifted phycobilisomes from Halomicronema hongdechloris</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Red-shifted phycobilisomes from Halomicronema hongdechloris</name>
                <oligomeric_state>Two APC trimers linked with APC E</oligomeric_state>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>APC phycobilisome complex</name>
                <natural_source database="NCBI">
                    <organism>Halomicronema hongdechloris</organism>
                </natural_source>
                <details>Taxonomy ID 1209493</details>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <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">
                    <buffer>
                        <ph>7.5</ph>
                        <details>0.8 M phosphate buffer</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <details>2% uranyl acetate for 2-3 seconds</details>
                    </staining>
                    <grid>
                        <details>200 mesh gold grid with thin carbon support</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>OTHER</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>TUNGSTEN HAIRPIN</electron_source>
                    <acceleration_voltage units="kV">100</acceleration_voltage>
                    <nominal_defocus_max units="&#181;m">3.0</nominal_defocus_max>
                    <nominal_magnification>180000.0</nominal_magnification>
                    <specimen_holder_model>PHILIPS ROTATION HOLDER</specimen_holder_model>
                    <date>2015-06-08</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GENERIC IMAGE PLATES</film_or_detector_model>
                            <number_real_images>12</number_real_images>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
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            <singleparticle_processing image_processing_id="1">
                <details>Semiautomatic selection using e2boxer.py swarm function</details>
                <ctf_correction>
                    <details>Each particle</details>
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                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">26.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN2</name>
                        </software>
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                    <number_images_used>420</number_images_used>
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                <final_two_d_classification>
                    <number_classes>32</number_classes>
                </final_two_d_classification>
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            <beta units="deg">90.0</beta>
            <gamma units="deg">90.0</gamma>
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        <axis_order>
            <fast>X</fast>
            <medium>Y</medium>
            <slow>Z</slow>
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        <statistics>
            <minimum>-0.16323277</minimum>
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        <contour_list>
            <contour primary="true">
                <level>0.86</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of red-shifted phycobiliprotein complex</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6430::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>4PO5</access_code>
                    <chain>
                        <chain_id>A</chain_id>
                    </chain>
                    <chain>
                        <chain_id>B</chain_id>
                    </chain>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>Chimera</name>
                    </software>
                </software_list>
                <details>Two trimers were fitted to each end of the EM map. 98% of atoms fit within the map at contour level 0.87.</details>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
        <figure_list>
            <figure>
                <file>emd_6430.jpg</file>
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                        <sec>60</sec>
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                    <annotation_details>Mask volume for reconstruction</annotation_details>
                    <details>::::EMDATABANK.org::::</details>
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            <file>emd_6430_fsc.xml</file>
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