<emd emdb_id="EMD-5665" 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>2013-05-02</deposition>
            <header_release>2013-07-03</header_release>
            <map_release>2014-06-25</map_release>
            <update>2014-10-22</update>
        </key_dates>
        <title>Cryo-EM structure of beta-hydroxyhexaketide-PikAIII conformation 1</title>
        <authors_list>
            <author>Whicher JR</author>
            <author>Dutta S</author>
            <author>Hansen DA</author>
            <author>Hale WA</author>
            <author>Chemler JA</author>
            <author>Narayan AR</author>
            <author>Hakansson K</author>
            <author>Sherman DH</author>
            <author>Smith JL</author>
            <author>Skiniotis G</author>
        </authors_list>
        <keywords>Type I polyketide synthase module</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Whicher JR</author>
                    <author order="2">Dutta S</author>
                    <author order="3">Hansen DA</author>
                    <author order="4">Hale WA</author>
                    <author order="5">Chemler JA</author>
                    <author order="6">Dosey AM</author>
                    <author order="7">Narayan ARH</author>
                    <author order="8">Hakansson K</author>
                    <author order="9">Sherman DH</author>
                    <author order="10">Smith JL</author>
                    <author order="11">Skiniotis G</author>
                    <title>Structural rearrangements of a polyketide synthase module during its catalytic cycle</title>
                    <journal>NATURE</journal>
                    <volume>510</volume>
                    <first_page>560</first_page>
                    <last_page>564</last_page>
                    <year>2014</year>
                    <external_references type="PUBMED">24965656</external_references>
                    <external_references type="DOI">doi:10.1038/nature13409</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>The 5th module from the pikromycin biosynthetic pathway (PikAIII) incubated with NADPH, methylmalonyl-CoA, and thiophenol-pentaketide</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>The 5th module from the pikromycin biosynthetic pathway (PikAIII) incubated with NADPH, methylmalonyl-CoA, and thiophenol-pentaketide</name>
                <details>Sample was not frozen prior to loading on the grid. The sample was monodisperse.</details>
                <oligomeric_state>Dimer</oligomeric_state>
                <number_unique_components>4</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">0.328</experimental>
                    <theoretical units="MDa">0.328</theoretical>
                    <method>Gel filtration chromatography</method>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>PikAIII</name>
                <natural_source database="NCBI">
                    <organism ncbi="54571">Streptomyces venezuelae</organism>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">0.328</experimental>
                    <theoretical units="MDa">0.328</theoretical>
                </molecular_weight>
                <number_of_copies>2</number_of_copies>
                <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_plasmid>pET28b</recombinant_plasmid>
                </recombinant_expression>
                <sequence>
                    <external_references type="UNIPROTKB">Q9ZGI3</external_references>
                </sequence>
            </protein_or_peptide>
            <ligand macromolecule_id="2">
                <name>NADPH</name>
                <natural_source database="NCBI">
                    <organism ncbi="32644">unidentified</organism>
                </natural_source>
                <number_of_copies>1</number_of_copies>
                <oligomeric_state>Monomer</oligomeric_state>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
            </ligand>
            <ligand macromolecule_id="3">
                <name>Methylmalonyl-CoA</name>
                <natural_source database="NCBI">
                    <organism ncbi="32644">unidentified</organism>
                </natural_source>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
            </ligand>
            <ligand macromolecule_id="4">
                <name>Thiophenol-pentaketide</name>
                <natural_source database="NCBI">
                    <organism ncbi="32644">unidentified</organism>
                </natural_source>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
            </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">0.1</concentration>
                    <buffer>
                        <ph>7.4</ph>
                        <details>50 mM HEPES, 100mM NaCl</details>
                    </buffer>
                    <grid>
                        <details>Glow-discharged Quantifoil R2/200 mesh grid</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">89</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <method>Blot for 1.5-2.0 seconds before plunging.</method>
                    </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">120</acceleration_voltage>
                    <nominal_cs units="mm">2</nominal_cs>
                    <nominal_defocus_min units="&#181;m">1.5</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">3.5</nominal_defocus_max>
                    <nominal_magnification>50000.0</nominal_magnification>
                    <calibrated_magnification>66964.0</calibrated_magnification>
                    <specimen_holder_model>OTHER</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">89</temperature_min>
                        <temperature_max units="K">89</temperature_max>
                    </temperature>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>Objective lens astigmatism was corrected at 135,000 times magnification.</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <date>2011-03-09</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN ULTRASCAN 4000 (4k x 4k)</film_or_detector_model>
                            <number_real_images>462</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">20</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>The particles were selected manually.</details>
                <ctf_correction>
                    <details>Each micrograph</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">10.7</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN1, EMAN2</name>
                        </software>
                    </software_list>
                    <number_images_used>24773</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="27649">
        <file>emd_5665.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>192</col>
            <row>192</row>
            <sec>192</sec>
        </dimensions>
        <origin>
            <col>-16</col>
            <row>-16</row>
            <sec>-16</sec>
        </origin>
        <spacing>
            <x>192</x>
            <y>192</y>
            <z>192</z>
        </spacing>
        <cell>
            <a units="&#8491;">430.08002</a>
            <b units="&#8491;">430.08002</b>
            <c units="&#8491;">430.08002</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>-11.509825709999999</minimum>
            <maximum>34.046489719999997</maximum>
            <average>0.0</average>
            <std>0.99999994</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.24</x>
            <y units="&#8491;">2.24</y>
            <z units="&#8491;">2.24</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>8.4</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of the 5th module from the pikromycin biosynthetic pathway (PikAIII) incubated with NADPH, methylmalonyl-CoA, and thiophenol-pentaketide.</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5665::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>2HG4</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>
                <refinement_space>REAL</refinement_space>
            </modelling>
            <modelling>
                <initial_model>
                    <access_code>2FR0</access_code>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>Chimera</name>
                    </software>
                </software_list>
                <refinement_space>REAL</refinement_space>
            </modelling>
            <modelling>
                <initial_model>
                    <access_code>2JU1</access_code>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>Chimera</name>
                    </software>
                </software_list>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>