+Open data
-Basic information
Entry | Database: PDB / ID: 6imk | ||||||
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Title | The crystal structure of AsfvLIG:CG 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 / MOLECULAR REPLACEMENT / Resolution: 2.502 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 | 6imk.cif.gz | 124.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6imk.ent.gz | 90.7 KB | Display | PDB format |
PDBx/mmJSON format | 6imk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6imk_validation.pdf.gz | 447.2 KB | Display | wwPDB validaton report |
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Full document | 6imk_full_validation.pdf.gz | 449.9 KB | Display | |
Data in XML | 6imk_validation.xml.gz | 18 KB | Display | |
Data in CIF | 6imk_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/im/6imk ftp://data.pdbj.org/pub/pdb/validation_reports/im/6imk | HTTPS FTP |
-Related structure data
Related structure data | 6imjSC 6imlC 6imnC 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: 48320.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) African swine fever virus / Gene: NP419L / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0A1E0U0 |
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#2: DNA chain | Mass: 6643.284 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 3719.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 3101.028 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#5: Water | ChemComp-HOH / |
-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: 50.97 % |
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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, 10% w/v PEG 10000, 0.1 M Ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 27, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 21031 / % possible obs: 98.5 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 17.25 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.67 / Num. unique obs: 2046 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IMJ Resolution: 2.502→29.674 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 27.93
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.502→29.674 Å
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Refine LS restraints |
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LS refinement shell |
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