+Open data
-Basic information
Entry | Database: PDB / ID: 5xm9 | ||||||
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Title | Crystal structure of AsfvPolX in complex with DNA enzyme. | ||||||
Components |
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Keywords | TRANSFERASE/DNA / PolX / DNA enzyme / complex / 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: 3.053 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 | 5xm9.cif.gz | 219.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xm9.ent.gz | 168.4 KB | Display | PDB format |
PDBx/mmJSON format | 5xm9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/5xm9 ftp://data.pdbj.org/pub/pdb/validation_reports/xm/5xm9 | HTTPS FTP |
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-Related structure data
Related structure data | 5xm8C 5xmaC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20551.684 Da / Num. of mol.: 4 / Mutation: D51N 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.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 7194.659 Da / Num. of mol.: 2 / 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: 2.93 Å3/Da / Density % sol: 57.96 % / Description: rod |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M di-ammonium hydrogen phosphate and 20% PEG 3350 |
-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: May 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→30 Å / Num. obs: 26143 / % possible obs: 97.5 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 3.05→3.16 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2408 / % possible all: 90.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HRB Resolution: 3.053→29.719 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 27.29
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.053→29.719 Å
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Refine LS restraints |
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LS refinement shell |
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