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- PDB-5xm9: Crystal structure of AsfvPolX in complex with DNA enzyme. -

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Basic information

Entry
Database: PDB / ID: 5xm9
TitleCrystal structure of AsfvPolX in complex with DNA enzyme.
Components
  • DNA (23-mer)
  • DNA (36-MER)
  • Repair DNA polymerase X
KeywordsTRANSFERASE/DNA / PolX / DNA enzyme / complex / TRANSFERASE-DNA complex
Function / homology
Function and homology information


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
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, thumb domain superfamily / DNA polymerase beta thumb ...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, thumb domain superfamily / DNA polymerase beta thumb / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Repair DNA polymerase X
Similarity search - Component
Biological speciesAfrican swine fever virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.053 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 (23-mer)
C: Repair DNA polymerase X
D: Repair DNA polymerase X
G: DNA (36-MER)
H: DNA (23-mer)


Theoretical massNumber of molelcules
Total (without water)118,5748
Polymers118,5748
Non-polymers00
Water00
1
A: Repair DNA polymerase X
B: Repair DNA polymerase X
E: DNA (36-MER)
F: DNA (23-mer)


Theoretical massNumber of molelcules
Total (without water)59,2874
Polymers59,2874
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Repair DNA polymerase X
D: Repair DNA polymerase X
G: DNA (36-MER)
H: DNA (23-mer)


Theoretical massNumber of molelcules
Total (without water)59,2874
Polymers59,2874
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.940, 118.878, 235.955
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Repair DNA polymerase X / Pol X


Mass: 20551.684 Da / Num. of mol.: 4 / Mutation: D51N
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.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (23-mer)


Mass: 7194.659 Da / Num. of mol.: 2 / 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: 2.93 Å3/Da / Density % sol: 57.96 % / Description: rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M di-ammonium hydrogen phosphate and 20% PEG 3350

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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: May 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.05→30 Å / Num. obs: 26143 / % possible obs: 97.5 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 20.4
Reflection shellResolution: 3.05→3.16 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2408 / % possible all: 90.5

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HRB

5hrb


Resolution: 3.053→29.719 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 27.29
RfactorNum. reflection% reflection
Rfree0.2776 1327 5.08 %
Rwork0.2154 --
obs0.2188 26143 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.053→29.719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5736 2414 0 0 8150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018544
X-RAY DIFFRACTIONf_angle_d1.24712006
X-RAY DIFFRACTIONf_dihedral_angle_d23.773464
X-RAY DIFFRACTIONf_chiral_restr0.0831380
X-RAY DIFFRACTIONf_plane_restr0.0051066
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0532-3.17530.35491250.31122547X-RAY DIFFRACTION91
3.1753-3.31970.2871330.27092649X-RAY DIFFRACTION94
3.3197-3.49440.29631590.23482659X-RAY DIFFRACTION95
3.4944-3.7130.31111540.23352757X-RAY DIFFRACTION98
3.713-3.9990.28741350.22782777X-RAY DIFFRACTION99
3.999-4.40030.22831590.18842770X-RAY DIFFRACTION99
4.4003-5.03440.24261510.18762835X-RAY DIFFRACTION100
5.0344-6.33270.28271530.19142854X-RAY DIFFRACTION100
6.3327-29.72090.18921580.16042968X-RAY DIFFRACTION100

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