<?xml version="1.0" encoding="UTF-8"?>
<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_2_0/emdb.xsd" emdb_id="EMD-0245" version="3.0.2.0">
    <admin>
        <current_status>
            <date>2020-11-25</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2018-09-13</deposition>
            <header_release>2018-09-26</header_release>
            <map_release>2018-10-17</map_release>
            <update>2020-11-25</update>
        </key_dates>
        <title>Structure of the in vitro assembled bacteriophage phi6 P1P4 complex</title>
        <authors_list>
            <author>Huiskonen JT</author>
            <author>Ilca SL</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Sun X</author>
                    <author order="2">Ilca SL</author>
                    <author order="3">Huiskonen JT</author>
                    <author order="4">Poranen MM</author>
                    <title>Dual Role of a Viral Polymerase in Viral Genome Replication and Particle Self-Assembly.</title>
                    <journal_abbreviation>MBio</journal_abbreviation>
                    <country>US</country>
                    <volume>9</volume>
                    <year>2018</year>
                    <external_references type="PUBMED">30279282</external_references>
                    <external_references type="DOI">doi:10.1128/mBio.01242-18</external_references>
                    <external_references type="ISSN">2150-7511</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-3185</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-0245</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Pseudomonas phage phi6</name>
        <supramolecule_list>
            <virus_supramolecule supramolecule_id="1">
                <name>Pseudomonas phage phi6</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>2</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <sci_species_name ncbi="10879">Pseudomonas phage phi6</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="317">Pseudomonas syringae</organism>
                </natural_host>
                <host_system database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_strain>JM109</recombinant_strain>
                </host_system>
                <virus_type>VIRUS-LIKE PARTICLE</virus_type>
                <virus_isolate>OTHER</virus_isolate>
                <virus_enveloped>false</virus_enveloped>
                <virus_empty>true</virus_empty>
            </virus_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>P1 protein from bacteriophage phi6</name>
                <natural_source database="NCBI">
                    <organism ncbi="10879">Pseudomonas phage phi6</organism>
                </natural_source>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <enantiomer>DEXTRO</enantiomer>
                <sequence>
                    <string>
MFNLKVKDLNGSARGLTQAFAIGELKNQLSVGALQLPLQFTRTFSASMTS

ELLWEVGKGNIDPVMYARLFFQYAQAGGALSVDELVNQFTEYHQSTACNP

EIWRKLTAYITGSSNRAIKADAVGKVPPTAILEQLRTLAPSEHELFHHIT

TDFVCHVLSPLGFILPDAAYVYRVGRTATYPNFYALVDCVRASDLRRMLT

ALSSVDSKMLQATFKAKGALAPALISQHLANAATTAFERSRGNFDANAVV

SSVLTILGRLWSPSTPKELDPSARLRNTNGIDQLRSNLALFIAYQDMVKQ

RGRAEVIFSDEELSSTIIPWFIEAMSEVSPFKLRPINETTSYIGQTSAID

HMGQPSHVVVYEDWQFAKEITAFTPVKLANNSNQRFLDVEPGISDRMSAT

LAPIGNTFAVSAFVKNRTAVYEAVSQRGTVNSNGAEMTLGFPSVVERDYA

LDRDPMVAIAALRTGIVDESLEARASNDLKRSMFNYYAAVMHYAVAHNPE

VVVSEHQGVAAEQGSLYLVWNVRTELRIPVGYNAIEGGSIRTPEPLEAIA

YNKPIQPSEVLQAKVLDLANHTTSIHIWPWHEASTEFAYEDAYSVTIRNK

RYTAEVKEFELLGLGQRRERVRILKPTVAHAIIQMWYSWFVEDDRTLAAA

RRTSRDDAEKLAIDGRRMQNAVTLLRKIEMIGTTGIGASAVHLAQSRIVD

QMAGRGLIDDSSDLHVGINRHRIRIWAGLAVLQMMGLLSRSEAEALTKVL

GDSNALGMVVATTDIDPSL</string>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>P4 protein from bacteriophage phi6</name>
                <natural_source database="NCBI">
                    <organism ncbi="10879">Pseudomonas phage phi6</organism>
                </natural_source>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <enantiomer>DEXTRO</enantiomer>
                <sequence>
                    <string>
MPIVVTQAHIDRVGIAADLLDASPVSLQVLGRPTAINTVVIKTYIAAVME

LASKQGGSLAGVDIRPSVLLKDTAIFTKPKAKSADVESDVDVLDTGIYSV

PGLARKPVTHRWPSEGIYSGVTALMGATGSGKSITLNEKLRPDVLIRWGE

VAEAYDELDTAVHISTLDEMLIVCIGLGALGFNVAVDSVRPLLFRLKGAA

SAGGIVAVFYSLLTDISNLFTQYDCSVVMVVNPMVDAEKIEYVFGQVMAS

TVGAILCADGNVSRTMFRTNKGRIFNGAAPLAADTHMPSMDRPTSMKALD

HTSIASVAPLERGSVDTDDRNSAPRRGANFSL</string>
                </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>8</ph>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <details></details>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_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">300</acceleration_voltage>
                    <nominal_cs units="mm">2.0</nominal_cs>
                    <specimen_holder_model>OTHER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <specialist_optics>
                        <energy_filter>
                            <name>GIF Quantum LS</name>
                            <slit_width units="eV">20</slit_width>
                        </energy_filter>
                    </specialist_optics>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K2 SUMMIT (4k x 4k)</film_or_detector_model>
                            <detector_mode>SUPER-RESOLUTION</detector_mode>
                            <digitization_details/>
                            <average_electron_dose_per_image units="e/Å^2">1.0</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>
                <particle_selection>
                    <number_selected>6878</number_selected>
                </particle_selection>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>RELION</name>
                        </software>
                    </software_list>
                </ctf_correction>
                <startup_model type_of_model="EMDB MAP">
                    <emdb_id>EMD-3185</emdb_id>
                </startup_model>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>I</point_group>
                    </applied_symmetry>
                    <algorithm>FOURIER SPACE</algorithm>
                    <resolution units="Å" res_type="BY AUTHOR">4.8</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                        </software>
                    </software_list>
                    <number_images_used>6857</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                        </software>
                    </software_list>
                </final_angle_assignment>
                <final_three_d_classification>
                    <software_list>
                        <software>
                            <name>RELION</name>
                        </software>
                    </software_list>
                </final_three_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="442369">
        <file>emd_0245.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>480</col>
            <row>480</row>
            <sec>480</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>480</x>
            <y>480</y>
            <z>480</z>
        </spacing>
        <cell>
            <a units="Å">648.0</a>
            <b units="Å">648.0</b>
            <c units="Å">648.0</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>-0.025962658</minimum>
            <maximum>0.07378059</maximum>
            <average>0.00092696014</average>
            <std>0.0058279634</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>0.02</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-0245::::</label>
        <annotation_details>Bacteriophage phi6 in vitro assembled P1P4 particle</annotation_details>
    </map>
    <interpretation>
        <segmentation_list>
            <segmentation>
                <file>emd_0245_msk_1.map</file>
            </segmentation>
        </segmentation_list>
    </interpretation>
</emd>
