<?xml version="1.0" encoding="UTF-8"?>
<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="https://ftp.ebi.ac.uk/pub/databases/em_ebi/emdb_related/emdb-schemas/emdb_schemas/v3/v3_0_9_3/emdb.xsd" version="3.0.9.3" emdb_id="EMD-0992">
    <admin>
        <current_status>
            <date>2024-05-29</date>
            <code>REL</code>
            <processing_site>PDBj</processing_site>
        </current_status>
        <sites>
            <deposition>PDBj</deposition>
            <last_processing>PDBj</last_processing>
        </sites>
        <key_dates>
            <deposition>2020-02-02</deposition>
            <header_release>2021-02-03</header_release>
            <map_release>2021-02-03</map_release>
            <update>2024-05-29</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Natural Science Foundation of China (NSFC)</funding_body>
                <code>31670749</code>
                <country>China</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Natural Science Foundation of China (NSFC)</funding_body>
                <code>31925024</code>
                <country>China</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Chinese Academy of Sciences</funding_body>
                <code>ZDBS-LY-SM003-02; XDB08020302</code>
                <country>China</country>
            </grant_reference>
        </grant_support>
        <title>Cryo-EM structure of the multiple peptide resistance factor (MprF) loaded with one lysyl-phosphatidylglycerol molecule</title>
        <authors_list>
            <author>Song DF</author>
            <author>Jiao HZ</author>
        </authors_list>
        <keywords>bacteria membrane protein, MEMBRANE PROTEIN</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author ORCID="0000-0001-6785-173X" order="1">Song D</author>
                    <author order="2">Jiao H</author>
                    <author ORCID="0000-0001-5502-9474" order="3">Liu Z</author>
                    <title>Phospholipid translocation captured in a bifunctional membrane protein MprF.</title>
                    <journal_abbreviation>Nat Commun</journal_abbreviation>
                    <country>UK</country>
                    <volume>12</volume>
                    <first_page>2927</first_page>
                    <last_page>2927</last_page>
                    <year>2021</year>
                    <external_references type="PUBMED">34006869</external_references>
                    <external_references type="DOI">doi:10.1038/s41467-021-23248-z</external_references>
                    <external_references type="ISSN">2041-1723</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>6lvf</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>bacterial membrane protein</name>
        <supramolecule_list>
            <cell_supramolecule supramolecule_id="1">
                <name>bacterial membrane protein</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <details>A recombinant protein from Rhizobium tropici expressed in Escherichia coli cells</details>
                <natural_source database="NCBI">
                    <organism ncbi="398">Rhizobium tropici</organism>
                </natural_source>
            </cell_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Low pH-inducible protein LpiA</name>
                <natural_source database="NCBI">
                    <organism ncbi="698761">Rhizobium tropici CIAT 899</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.096094672</theoretical>
                </molecular_weight>
                <number_of_copies>2</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MSSPIDLESADEELEERGGIVGLLNRYRALIVAVLTVAVFCIAAYAIYDLTTEVRYDDVVHALTTTKISSVLLALLFTGL
SFASLIFYDQNALEYIGKRLPFPHVALTSFSAYAVGNTAGFGALSAGAIRYRAYTRLGLSPDDITRVIAFVTLAFGLGLA
SVGAMALLVIADEIGPLISVDGLWLRLIAIAILAALAFVVYAGRNGREVRIGPVAVRLPDSRTWSRQFLVTAFDIAASAS
VLYVLLPETSIGWPGFFAIYAIAVGLGVLSHVPAGFGVFETIIIAWLGSSVNEDAVLSSLVLYRVIYNVIPLVIAIAAIS
VAELRRFVDHPVASSMRRIGARLMPQLLSAFALLLGMMLVFSSVTPTPDHNLIVLSDYLPLSLVESAHFLSSLLGLAIIV
AARGLSQRLDGAWWVSTFSALFALFFSLLKAIAIVEAGLLAFFVFSLVVSRRLFKRPASLLNQTLTAGWLTAIAVVCIGA
IVVLFFVYRDVGYSNELWWQFEFADEAPRGLRAALGISIVSSAIAIFSLLRPATKRPEPVSDDAVARAVEIVRKQGVADA
NLVRMGDKSIMFSEKGDAFIMYGKQGRSWIALFDPVGPRQALPDLIWRFVETARAAGCRSVFYQISPALLSYCADAGLRA
FKLGELAVVNLANFELKGGKWANLRQTASRAVRDGLEFAVIEPQDIPDVLDQLAHVSDTWLADHNAKEKSFSLGAFDPDY
VCSQPVGVLKKDGKIVAFANILMTETKEEGSVDLMRFSPDAPKGSMDFLFVQILEYLKGEGFQRFNLGMAPLSGMSRRES
APVWDRVGGTVFEHGERFYNFKGLRAFKSKFHPEWQPRYLAVSGGVSPMIALMDATFLIGGGLKGVVRKKLAAALEHHHH
HH</string>
                    <external_references type="UNIPROTKB">L0LM43</external_references>
                </sequence>
            </protein_or_peptide>
            <ligand macromolecule_id="2">
                <name>[(2~{R})-3-[[(2~{S})-3-[(2~{S})-2,6-bis(azanyl)hexanoyl]oxy-2-oxidanyl-propoxy]-oxidanyl-phosphoryl]oxy-2-hexadecanoyloxy-propyl] hexadecanoate</name>
                <molecular_weight>
                    <theoretical units="MDa">0.000851142</theoretical>
                </molecular_weight>
                <number_of_copies>2</number_of_copies>
                <formula>EV9</formula>
            </ligand>
            <ligand macromolecule_id="3">
                <name>1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE</name>
                <molecular_weight>
                    <theoretical units="MDa">0.00072297</theoretical>
                </molecular_weight>
                <number_of_copies>2</number_of_copies>
                <formula>LHG</formula>
            </ligand>
            <ligand macromolecule_id="4">
                <name>(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE</name>
                <molecular_weight>
                    <theoretical units="MDa">0.000751023</theoretical>
                </molecular_weight>
                <number_of_copies>2</number_of_copies>
                <formula>PGT</formula>
            </ligand>
        </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">6</concentration>
                    <buffer>
                        <ph>7.5</ph>
                        <component>
                            <concentration units="mM">20.0</concentration>
                            <formula>Tris-HCl</formula>
                            <name>buffer</name>
                        </component>
                        <component>
                            <concentration units="mM">300.0</concentration>
                            <formula>NaCl</formula>
                            <name>salt</name>
                        </component>
                    </buffer>
                    <grid>
                        <model>Quantifoil R1.2/1.3</model>
                        <material>COPPER</material>
                        <mesh>300</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>HOLEY</film_topology>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                            <time units="s">60</time>
                            <atmosphere>OTHER</atmosphere>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">80</chamber_humidity>
                        <chamber_temperature units="K">291</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                    </vitrification>
                    <details>The protein is reconstituted in lipid nanodiscs</details>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TALOS ARCTICA</microscope>
                    <illumination_mode>OTHER</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">2.7</nominal_cs>
                    <nominal_defocus_min units="µm">1.5</nominal_defocus_min>
                    <nominal_defocus_max units="µm">2.0</nominal_defocus_max>
                    <nominal_magnification>130000.0</nominal_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <specialist_optics>
                        <energy_filter>
                            <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>
                                <frames_per_image>1-32</frames_per_image>
                            </digitization_details>
                            <number_grids_imaged>1</number_grids_imaged>
                            <number_real_images>2921</number_real_images>
                            <average_exposure_time units="s">5.2</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">50.0</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>887196</number_selected>
                </particle_selection>
                <startup_model type_of_model="OTHER">
                    <details>generated by cryoSPARC</details>
                </startup_model>
                <final_reconstruction>
                    <number_classes_used>1</number_classes_used>
                    <applied_symmetry>
                        <point_group>C2</point_group>
                    </applied_symmetry>
                    <resolution units="Å" res_type="BY AUTHOR">3.7</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>3.0</version>
                        </software>
                    </software_list>
                    <number_images_used>160417</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>COMMON LINE</type>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>COMMON LINE</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>3.0</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
                <final_three_d_classification>
                    <number_classes>8</number_classes>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>3.0</version>
                        </software>
                    </software_list>
                </final_three_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="32001">
        <file>emd_0992.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>200</col>
            <row>200</row>
            <sec>200</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>200</x>
            <y>200</y>
            <z>200</z>
        </spacing>
        <cell>
            <a units="Å">200.0</a>
            <b units="Å">200.0</b>
            <c units="Å">200.0</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>-0.11533239</minimum>
            <maximum>0.18517745</maximum>
            <average>0.00060421997</average>
            <std>0.0052326815</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.0</x>
            <y units="Å">1.0</y>
            <z units="Å">1.0</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.0239</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-0992::::</label>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <refinement_protocol>AB INITIO MODEL</refinement_protocol>
                <target_criteria>Correlation coefficient</target_criteria>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
