+Open data
-Basic information
Entry | Database: PDB / ID: 5hrd | ||||||
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Title | The crystal structure of AsfvPolX:DNA2 binary complex | ||||||
Components |
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Keywords | TRANSFERASE/DNA / ASFV / PolX / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information virion component / base-excision repair / double-strand break repair via nonhomologous end joining / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | African swine fever virus synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Chen, Y.Q. / Zhang, J. / Gan, J.H. | ||||||
Citation | Journal: To Be Published Title: The crystal structure of Se-AsfvPolX(L52/163M mutant) in complex with 1nt-gap DNA1 Authors: Chen, Y.Q. / Zhang, J. / Gan, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hrd.cif.gz | 345 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hrd.ent.gz | 275.7 KB | Display | PDB format |
PDBx/mmJSON format | 5hrd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/5hrd ftp://data.pdbj.org/pub/pdb/validation_reports/hr/5hrd | HTTPS FTP |
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-Related structure data
Related structure data | 5hr9SC 5hrbC 5hreC 5hrfC 5hrgC 5hrhC 5hrkC 5hrlC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 20609.723 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) African swine fever virus / Gene: O174L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0A1E3N6, UniProt: P42494*PLUS #2: DNA chain | Mass: 2467.629 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.94 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M Succinic acid PH 7.0, 15% PGE 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 75045 / % possible obs: 93.5 % / Redundancy: 3.2 % / Net I/σ(I): 20.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HR9 Resolution: 1.8→29.31 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 10.558 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.826 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→29.31 Å
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Refine LS restraints |
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