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- PDB-2m2u: Binary complex of African Swine Fever Virus Pol X with MgdGTP -

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Basic information

Entry
Database: PDB / ID: 2m2u
TitleBinary complex of African Swine Fever Virus Pol X with MgdGTP
ComponentsRepair DNA polymerase X
KeywordsTRANSFERASE / DNA polymerase / Nucleotidyl Transferase
Function / homology
Function and homology information


virion component / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / DNA binding / metal ion binding
Similarity search - Function
Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase beta thumb / DNA polymerase, thumb domain superfamily ...Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase beta thumb / DNA polymerase, thumb domain superfamily / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Repair DNA polymerase X
Similarity search - Component
Biological speciesAfrican swine fever virus
MethodSOLUTION NMR / distance geometry
Model detailslowest energy, model 1
AuthorsWu, W. / Su, M. / Tsai, M.
CitationJournal: 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
DepositionJan 3, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Repair DNA polymerase X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9074
Polymers20,3511
Non-polymers5563
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 2000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Repair DNA polymerase X / Pol X


Mass: 20351.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus / Plasmid: pET-17b / Production host: Escherichia coli (E. coli) / References: UniProt: P42494, DNA-directed DNA polymerase
#2: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Deoxyguanosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1323D HNCO
1423D HNCA
1523D HN(CA)CB
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY aliphatic
1912D 1H-13C HSQC aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 13C; U-100% 15N] protein_1, 5 mM [U-100% 13C; U-100% 15N] 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, 10 mM MG2, 10 mM [U-100% 2H] DTT, 50 mM Borate, 50 mM potassium chloride, 95% H2O/5% D2O95% H2O/5% D2O
20.5 mM [U-13C; U-15N; U-2H] protein_1, 5 mM 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, 10 mM MG2, 10 mM [U-100% 2H] DTT, 50 mM Borate, 50 mM potassium chloride, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMentity_1-1[U-100% 13C; U-100% 15N]1
5 mM2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE-2[U-100% 13C; U-100% 15N]1
10 mMMG2-31
10 mMDTT-4[U-100% 2H]1
50 mMBorate-51
50 mMpotassium chloride-61
0.5 mMentity_1-7[U-13C; U-15N; U-2H]2
5 mM2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE-82
10 mMMG2-92
10 mMDTT-10[U-100% 2H]2
50 mMBorate-112
50 mMpotassium chloride-122
Sample conditionsIonic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance8001
Bruker AvanceBrukerAvance8502
Bruker AvanceBrukerAvance6003

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
HaddockDr. Alexandre Bonvinrefinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR constraintsNOE constraints total: 3066 / NOE intraresidue total count: 1359 / NOE long range total count: 605 / NOE medium range total count: 543 / NOE sequential total count: 541 / Protein phi angle constraints total count: 155 / Protein psi angle constraints total count: 155
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 2000 / Conformers submitted total number: 20
NMR ensemble rmsDistance rms dev: 0.07 Å / Distance rms dev error: 0.01 Å

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