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Open data
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Basic information
Entry | Database: PDB / ID: 6imk | ||||||
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Title | The crystal structure of AsfvLIG:CG complex | ||||||
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![]() | LIGASE/DNA / AsfvLIG with C:G complex / LIGASE-DNA complex / DNA BINDING PROTEIN | ||||||
Function / homology | ![]() DNA ligase (ATP) activity / virion component / DNA recombination / DNA replication / DNA repair / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, Y.Q. / Gan, J.H. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124.8 KB | Display | ![]() |
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PDB format | ![]() | 90.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.2 KB | Display | ![]() |
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Full document | ![]() | 449.9 KB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 25 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6imjSC ![]() 6imlC ![]() 6imnC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() |
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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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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