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Yorodumi- PDB-2m2v: African Swine Fever Virus Pol X in the ternary complex with MgdGT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2m2v | ||||||
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Title | African Swine Fever Virus Pol X in the ternary complex with MgdGTP and DNA | ||||||
Components | Repair DNA polymerase X | ||||||
Keywords | TRANSFERASE / DNA polymerase / Nucleotidyl Transferase | ||||||
Function / homology | Function and homology information base-excision repair / virion component / 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 | ||||||
Method | SOLUTION NMR / distance geometry | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Wu, W. / Su, M. / Tsai, M. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2014 Title: How a low-fidelity DNA polymerase chooses non-Watson-Crick from Watson-Crick incorporation. Authors: Wu, W.J. / Su, M.I. / Wu, J.L. / Kumar, S. / Lim, L.H. / Wang, C.W. / Nelissen, F.H. / Chen, M.C. / Doreleijers, J.F. / Wijmenga, S.S. / Tsai, M.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2m2v.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2m2v.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 2m2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2m2v_validation.pdf.gz | 541.7 KB | Display | wwPDB validaton report |
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Full document | 2m2v_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2m2v_validation.xml.gz | 182.7 KB | Display | |
Data in CIF | 2m2v_validation.cif.gz | 146.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/2m2v ftp://data.pdbj.org/pub/pdb/validation_reports/m2/2m2v | HTTPS FTP |
-Related structure data
Related structure data | 2m2tC 2m2uC 2m2wC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 20351.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) African swine fever virus / Production host: Escherichia coli (E. coli) / References: UniProt: P42494, DNA-directed DNA polymerase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.5 mM ILV-CH3-[U-13C; U-15N; U-2H] protein, 10 mM Mg, 4 mM dGTP, 0.6 mM [U-100% 13C; U-100% 15N] DNA, 50 mM Borate, 10 mM [U-2H] DTT, 200 mM potassium chloride, 95% H2O/5% D2O Solvent system: 95% H2O/5% D2O | ||||||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 250 / pH: 6.5 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: distance geometry / Software ordinal: 1 | |||||||||
NMR constraints | NOE constraints total: 3030 / NOE intraresidue total count: 1356 / NOE long range total count: 431 / NOE medium range total count: 533 / NOE sequential total count: 710 / Protein phi angle constraints total count: 155 / Protein psi angle constraints total count: 155 | |||||||||
NMR representative | Selection criteria: lowest energy | |||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 2000 / Conformers submitted total number: 20 |