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- PDB-5xma: Crystal structure of AsfvPolX in complex with DNA enzyme at P4321... -

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Basic information

Entry
Database: PDB / ID: 5xma
TitleCrystal structure of AsfvPolX in complex with DNA enzyme at P43212 space group
Components
  • DNA (36-MER)
  • DNA/RNA (5'-D(*AP*CP*GP*AP*GP*AP*GP*AP*GP*AP*T)-R(P*G)-D(P*GP*GP*TP*GP*CP*GP*TP*TP*AP*CP*A)-3')
  • Repair DNA polymerase X
KeywordsTRANSFERASE/DNA / PolX / DNA enzyme / complex / TRANSFERASE-DNA complex
Function / homology
Function and homology information


virion component / base-excision repair / 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
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
DNA / DNA (> 10) / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / Repair DNA polymerase X
Similarity search - Component
Biological speciesAfrican swine fever virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsLiu, H.H. / Gan, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
Key Research and Development Project of China2016YFA0500600 China
CitationJournal: Nat Commun / Year: 2017
Title: Crystal structure of an RNA-cleaving DNAzyme.
Authors: Liu, H. / Yu, X. / Chen, Y. / Zhang, J. / Wu, B. / Zheng, L. / Haruehanroengra, P. / Wang, R. / Li, S. / Lin, J. / Li, J. / Sheng, J. / Huang, Z. / Ma, J. / Gan, J.
History
DepositionMay 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Repair DNA polymerase X
B: Repair DNA polymerase X
E: DNA (36-MER)
F: DNA/RNA (5'-D(*AP*CP*GP*AP*GP*AP*GP*AP*GP*AP*T)-R(P*G)-D(P*GP*GP*TP*GP*CP*GP*TP*TP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)59,3054
Polymers59,3054
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-17 kcal/mol
Surface area26680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.846, 78.846, 241.677
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Repair DNA polymerase X / Pol X


Mass: 20552.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus (strain Badajoz 1971 Vero-adapted)
Strain: Badajoz 1971 Vero-adapted / Gene: Ba71V-97, O174L / Production host: Escherichia coli (E. coli) / References: UniProt: P42494, DNA-directed DNA polymerase
#2: DNA chain DNA (36-MER)


Mass: 10989.054 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA/RNA hybrid DNA/RNA (5'-D(*AP*CP*GP*AP*GP*AP*GP*AP*GP*AP*T)-R(P*G)-D(P*GP*GP*TP*GP*CP*GP*TP*TP*AP*CP*A)-3')


Mass: 7210.659 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.16 % / Description: diamond
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M Tris pH 7.0, 15% v/v ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.8→30 Å / Num. obs: 7857 / % possible obs: 96.8 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.2
Reflection shellResolution: 3.8→3.94 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 734 / % possible all: 92.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HRB

5hrb


Resolution: 3.8→29.353 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 33.2
RfactorNum. reflection% reflection
Rfree0.2854 359 4.57 %
Rwork0.2584 --
obs0.2596 7857 97.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.8→29.353 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2818 1208 0 0 4026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034237
X-RAY DIFFRACTIONf_angle_d0.5815977
X-RAY DIFFRACTIONf_dihedral_angle_d19.6652362
X-RAY DIFFRACTIONf_chiral_restr0.04693
X-RAY DIFFRACTIONf_plane_restr0.003537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7985-4.34660.3351140.34992353X-RAY DIFFRACTION95
4.3466-5.47050.32331340.30192446X-RAY DIFFRACTION97
5.4705-29.35370.25191110.21462699X-RAY DIFFRACTION99

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