<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-1485" version="3.0.1.1" 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>PDBe</processing_site>
      </current_status>
      <sites>
         <deposition>PDBe</deposition>
         <last_processing>PDBe</last_processing>
      </sites>
      <key_dates>
         <deposition>2008-02-28</deposition>
         <header_release>2008-02-28</header_release>
         <map_release>2010-06-23</map_release>
         <update>2012-10-31</update>
      </key_dates>
      <title>The archaeal DNA Ligase-PCNA-DNA complex</title>
      <authors_list>
         <author>Mayanagi K</author>
         <author>Kiyonari S</author>
         <author>Ishino Y</author>
         <author>Shirai T</author>
         <author>Morikawa K</author>
      </authors_list>
      <keywords>
         </keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Mayanagi K</author>
               <author order="2">Kiyonari S</author>
               <author order="3">Saito M</author>
               <author order="4">Shirai T</author>
               <author order="5">Ishino Y</author>
               <author order="6">Morikawa K</author>
               <title>Mechanism of replication machinery assembly as revealed by the DNA ligase-PCNA-DNA complex architecture.</title>
               <journal>PROC.NAT.ACAD.SCI.USA</journal>
               <volume>106</volume>
               <first_page>4647</first_page>
               <last_page>4652</last_page>
               <year>2009</year>
               <external_references type="PUBMED">19255439</external_references>
               <external_references type="DOI">doi:10.1073/pnas.0811196106</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
   </crossreferences>
   <sample>
      <name>Pyrococcus furiosus DNA Ligase bound to PCNA and DNA</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>Pyrococcus furiosus DNA Ligase bound to PCNA and DNA</name>
            <details>The sample was monodisperse</details>
            <oligomeric_state>Heteropentamer</oligomeric_state>
            <number_unique_components>3</number_unique_components>
            <molecular_weight>
               <theoretical units="MDa">0.16</theoretical>
               <method>One DNA Ligase binds to three PCNA and one nicked DNA</method>
            </molecular_weight>
         </sample_supramolecule>
      </supramolecule_list>
      <macromolecule_list>
         <protein_or_peptide macromolecule_id="1">
            <name synonym="DNA Ligase">Pyrococcus furiosus DNA Ligase</name>
            <natural_source database="NCBI">
               <organism ncbi="2261">Pyrococcus furiosus</organism>
            </natural_source>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               </recombinant_expression>
            <sequence>
               </sequence>
         </protein_or_peptide>
         <protein_or_peptide macromolecule_id="2">
            <name synonym="PCNA">Proliferating cell nuclear antigen</name>
            <natural_source database="NCBI">
               <organism ncbi="2261">Pyrococcus furiosus</organism>
            </natural_source>
            <molecular_weight>
               <theoretical units="MDa">0.028</theoretical>
            </molecular_weight>
            <number_of_copies>3</number_of_copies>
            <oligomeric_state>Trimeric</oligomeric_state>
            <recombinant_exp_flag>true</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               </recombinant_expression>
            <sequence>
               </sequence>
         </protein_or_peptide>
         <dna macromolecule_id="3">
            <name synonym="DNA">PCNA-nicked DNA</name>
            <natural_source database="NCBI">
               <organism ncbi="32630">synthetic construct</organism>
            </natural_source>
            <classification>DNA</classification>
            <structure>DOUBLE HELIX</structure>
            <synthetic_flag>true</synthetic_flag>
         </dna>
      </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">0.02</concentration>
               <buffer>
                  <ph>6.5</ph>
                  <details>20 mM MES,50 mM NaCl,10 mM MgCl2,0.1 mM ATP</details>
               </buffer>
               <staining>
                  <type>NEGATIVE</type>
                  <details>The sample solution was applied to a copper grid supporting a continuous thin-carbon film, left for 1 min, then stained with 3 drops of 2% uranyl acetate, and air dried.</details>
               </staining>
               <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>JEOL 1010</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_cs units="mm">5.6</nominal_cs>
               <nominal_magnification>400000.0</nominal_magnification>
               <specimen_holder_model>OTHER</specimen_holder_model>
               <alignment_procedure>
                  <legacy>
                     <astigmatism>Objective lens astigmatism was corrected at 400,000 times magnification</astigmatism>
                  </legacy>
               </alignment_procedure>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="CCD">GENERIC GATAN</film_or_detector_model>
                     <number_real_images>400</number_real_images>
                  </image_recording>
               </image_recording_list>
               <specimen_holder>Eucentric</specimen_holder>
               <tilt_angle_min>0</tilt_angle_min>
               <tilt_angle_max>0</tilt_angle_max>
            </single_particle_microscopy>
         </microscopy_list>
         <singleparticle_processing image_processing_id="1">
            <final_reconstruction>
               <applied_symmetry>
                  <point_group>C1</point_group>
               </applied_symmetry>
               <algorithm>OTHER</algorithm>
               <resolution res_type="BY AUTHOR" units="&#8491;">17.0</resolution>
               <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
               <software_list>
                  <software>
                     <name>EMAN,IMAGIC</name>
                  </software>
               </software_list>
               <number_images_used>19544</number_images_used>
            </final_reconstruction>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="687">
      <file>emd_1485.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
      <dimensions>
         <col>56</col>
         <row>56</row>
         <sec>56</sec>
      </dimensions>
      <origin>
         <col>-28</col>
         <row>-28</row>
         <sec>-28</sec>
      </origin>
      <spacing>
         <x>56</x>
         <y>56</y>
         <z>56</z>
      </spacing>
      <cell>
         <a units="&#8491;">170.5</a>
         <b units="&#8491;">170.5</b>
         <c units="&#8491;">170.5</c>
         <alpha units="deg">90</alpha>
         <beta units="deg">90</beta>
         <gamma units="deg">90</gamma>
      </cell>
      <axis_order>
         <fast>X</fast>
         <medium>Y</medium>
         <slow>Z</slow>
      </axis_order>
      <statistics>
         <minimum>-1.62418</minimum>
         <maximum>8.66733</maximum>
         <average>0.000000000694363</average>
         <std>0.819917</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">3.1</x>
         <y units="&#8491;">3.1</y>
         <z units="&#8491;">3.1</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>1.19</level>
            <source>EMDB</source>
         </contour>
      </contour_list>
      <annotation_details>This is a map of DNA ligase-PCNA-DNA complex</annotation_details>
      <details>::::EMDATABANK.org::::EMD-1485::::</details>
   </map>
   <interpretation>
      <modelling_list>
         <modelling>
            <initial_model>
               <access_code>1GE8</access_code>
               <chain>
                  <chain_id>A</chain_id>
               </chain>
            </initial_model>
            <details>PDBEntryID_givenInChain.</details>
            <refinement_space>REAL</refinement_space>
         </modelling>
         <modelling>
            <initial_model>
               <access_code>2POL</access_code>
               <chain>
                  <chain_id>A</chain_id>
               </chain>
            </initial_model>
            <details>PDBEntryID_givenInChain.</details>
            <refinement_space>REAL</refinement_space>
         </modelling>
      </modelling_list>
   </interpretation>
</emd>