+Open data
-Basic information
Entry | Database: PDB / ID: 6imj | ||||||
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Title | The crystal structure of Se-AsfvLIG:DNA complex | ||||||
Components |
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Keywords | LIGASE/DNA / AsfvLIG with C:G complex / LIGASE-DNA complex / DNA BINDING PROTEIN | ||||||
Function / homology | Function and homology information DNA ligase (ATP) activity / virion component / DNA recombination / DNA replication / DNA repair / ATP binding Similarity search - Function | ||||||
Biological species | African swine fever virus synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.554 Å | ||||||
Authors | Chen, Y.Q. / Gan, J.H. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: Structure of the error-prone DNA ligase of African swine fever virus identifies critical active site residues. Authors: Chen, Y. / Liu, H. / Yang, C. / Gao, Y. / Yu, X. / Chen, X. / Cui, R. / Zheng, L. / Li, S. / Li, X. / Ma, J. / Huang, Z. / Li, 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 | 6imj.cif.gz | 369 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6imj.ent.gz | 306.9 KB | Display | PDB format |
PDBx/mmJSON format | 6imj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6imj_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6imj_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6imj_validation.xml.gz | 32.4 KB | Display | |
Data in CIF | 6imj_validation.cif.gz | 44.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/im/6imj ftp://data.pdbj.org/pub/pdb/validation_reports/im/6imj | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 48514.938 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) African swine fever virus / Gene: NP419L, AFSV47Ss_0152 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0A1E0U0 |
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-DNA chain , 2 types, 2 molecules CD
#2: DNA chain | Mass: 6840.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 6643.284 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 87 molecules
#4: Chemical | #5: Chemical | ChemComp-CD / #6: Chemical | ChemComp-CL / | #7: 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: 3.23 Å3/Da / Density % sol: 61.9 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M BIS-TRIS pH 5.5, 15% w/v PEG 100000.1 M Ammonium acetate, 0.1 M Cadmium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 1, 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: 2.55→30 Å / Num. obs: 44993 / % possible obs: 97.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.55→2.64 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 1.92 / Num. unique obs: 4370 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.554→29.936 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 28.55
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.554→29.936 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 33.8637 Å / Origin y: 2.0453 Å / Origin z: 29.919 Å
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Refinement TLS group | Selection details: all |