+Open data
-Basic information
Entry | Database: PDB / ID: 6lmj | ||||||||||||
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Title | ASFV pA104R in complex with double-strand DNA | ||||||||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / Complex / dsDNA / ASFV / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||||||||
Function / homology | Function and homology information virion component / structural constituent of chromatin / DNA replication / DNA binding Similarity search - Function | ||||||||||||
Biological species | African swine fever virus synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||||||||
Authors | Wang, H. / Qi, J. / Chai, Y. / Gao, F. / Liu, R. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: The structural basis of African swine fever virus pA104R binding to DNA and its inhibition by stilbene derivatives. Authors: Liu, R. / Sun, Y. / Chai, Y. / Li, S. / Li, S. / Wang, L. / Su, J. / Yu, S. / Yan, J. / Gao, F. / Zhang, G. / Qiu, H.J. / Gao, G.F. / Qi, J. / Wang, H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lmj.cif.gz | 134.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lmj.ent.gz | 101.2 KB | Display | PDB format |
PDBx/mmJSON format | 6lmj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lmj_validation.pdf.gz | 447.9 KB | Display | wwPDB validaton report |
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Full document | 6lmj_full_validation.pdf.gz | 451.4 KB | Display | |
Data in XML | 6lmj_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 6lmj_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lm/6lmj ftp://data.pdbj.org/pub/pdb/validation_reports/lm/6lmj | HTTPS FTP |
-Related structure data
Related structure data | 6lmhSC 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: 12459.636 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) African swine fever virus Gene: A104R, A104R CDS, BA71V-A104R, AFSV47Ss_0056, ASFV-Georgia_4-058 Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A1E0L7, UniProt: P68742*PLUS #2: DNA chain | Mass: 5800.768 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: 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: 2.63 Å3/Da / Density % sol: 53.26 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M imidazole malate, pH 7.0, 15% (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 9113 / % possible obs: 96.2 % / Redundancy: 6.4 % / CC1/2: 1 / Net I/σ(I): 20.619 |
Reflection shell | Resolution: 2.8→2.9 Å / Num. unique obs: 931 / CC1/2: 0.79 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LMH Resolution: 2.8→27.886 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.54
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→27.886 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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