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Yorodumi- PDB-5xma: Crystal structure of AsfvPolX in complex with DNA enzyme at P4321... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xma | ||||||
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Title | Crystal structure of AsfvPolX in complex with DNA enzyme at P43212 space group | ||||||
Components |
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Keywords | TRANSFERASE/DNA / PolX / DNA enzyme / complex / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information base-excision repair / virion component / 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: 3.8 Å | ||||||
Authors | Liu, H.H. / Gan, J.H. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2017 Title: Crystal structure of an RNA-cleaving DNAzyme. Authors: Liu, H. / Yu, X. / Chen, Y. / Zhang, J. / Wu, B. / Zheng, L. / Haruehanroengra, P. / Wang, R. / Li, S. / Lin, J. / Li, J. / Sheng, J. / Huang, Z. / Ma, J. / Gan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xma.cif.gz | 117.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xma.ent.gz | 84.9 KB | Display | PDB format |
PDBx/mmJSON format | 5xma.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xma_validation.pdf.gz | 434.1 KB | Display | wwPDB validaton report |
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Full document | 5xma_full_validation.pdf.gz | 437.9 KB | Display | |
Data in XML | 5xma_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 5xma_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/5xma ftp://data.pdbj.org/pub/pdb/validation_reports/xm/5xma | HTTPS FTP |
-Related structure data
Related structure data | 5xm8C 5xm9C 5hrbS 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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Unit cell |
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-Components
#1: Protein | Mass: 20552.668 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) African swine fever virus (strain Badajoz 1971 Vero-adapted) Strain: Badajoz 1971 Vero-adapted / Gene: Ba71V-97, O174L / Production host: Escherichia coli (E. coli) / References: UniProt: P42494, DNA-directed DNA polymerase #2: DNA chain | | Mass: 10989.054 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA/RNA hybrid | | Mass: 7210.659 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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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: 3.17 Å3/Da / Density % sol: 61.16 % / Description: diamond |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M Tris pH 7.0, 15% v/v ethanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→30 Å / Num. obs: 7857 / % possible obs: 96.8 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 3.8→3.94 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 734 / % possible all: 92.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HRB Resolution: 3.8→29.353 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 33.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.8→29.353 Å
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Refine LS restraints |
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LS refinement shell |
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