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- PDB-5xm8: Crystal structure of AsfvPolX in complex with DNA enzyme and Pb. -

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Basic information

Entry
Database: PDB / ID: 5xm8
TitleCrystal structure of AsfvPolX in complex with DNA enzyme and Pb.
Components
  • DNA (23-mer)
  • DNA (36-MER)
  • Repair DNA polymerase X
KeywordsTRANSFERASE/DNA / PolX / DNA enzyme / Pb / 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
LEAD (II) ION / PHOSPHATE ION / 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: 2.55 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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,16513
Polymers118,5788
Non-polymers5875
Water36020
1
A: Repair DNA polymerase X
B: Repair DNA polymerase X
E: DNA (36-MER)
F: DNA (23-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7818
Polymers59,2894
Non-polymers4924
Water724
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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3845
Polymers59,2894
Non-polymers951
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.727, 118.848, 235.979
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Repair DNA polymerase X / Pol X


Mass: 20552.668 Da / Num. of mol.: 4
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

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DNA chain , 2 types, 4 molecules EGFH

#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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Non-polymers , 3 types, 25 molecules

#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-PB / LEAD (II) ION / Lead


Mass: 207.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pb
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

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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: 2.92 Å3/Da / Density % sol: 57.86 % / Description: rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M di-ammonium hydrogen phosphate, 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: 2.55→30 Å / Num. obs: 45470 / % possible obs: 98.6 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.8
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4339 / % possible all: 95.5

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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: 2.55→29.712 Å / SU ML: 0.66 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 38.8
RfactorNum. reflection% reflection
Rfree0.2827 2284 5.08 %
Rwork0.2353 --
obs0.238 44952 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.55→29.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5768 2414 21 20 8223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038618
X-RAY DIFFRACTIONf_angle_d0.91612113
X-RAY DIFFRACTIONf_dihedral_angle_d21.6113485
X-RAY DIFFRACTIONf_chiral_restr0.041384
X-RAY DIFFRACTIONf_plane_restr0.0031075
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.60550.44441360.41792566X-RAY DIFFRACTION96
2.6055-2.6660.42951360.40352626X-RAY DIFFRACTION97
2.666-2.73270.41691280.39472580X-RAY DIFFRACTION97
2.7327-2.80650.37981490.38312582X-RAY DIFFRACTION98
2.8065-2.8890.40011300.35832662X-RAY DIFFRACTION98
2.889-2.98220.39981590.35092635X-RAY DIFFRACTION99
2.9822-3.08860.37231290.31472645X-RAY DIFFRACTION98
3.0886-3.21220.27531210.26452657X-RAY DIFFRACTION99
3.2122-3.35820.30251350.2332671X-RAY DIFFRACTION99
3.3582-3.5350.29381410.2312666X-RAY DIFFRACTION99
3.535-3.7560.32181410.22962675X-RAY DIFFRACTION100
3.756-4.04540.28381480.21942697X-RAY DIFFRACTION100
4.0454-4.45130.25831580.1832695X-RAY DIFFRACTION100
4.4513-5.09260.22541790.18832697X-RAY DIFFRACTION100
5.0926-6.40550.23361450.19462763X-RAY DIFFRACTION100
6.4055-29.7140.231490.16452851X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 20.2968 Å / Origin y: 29.8983 Å / Origin z: -42.0638 Å
111213212223313233
T0.8062 Å2-0.1252 Å20.0438 Å2-0.7663 Å2-0.03 Å2--0.5006 Å2
L-0.0726 °2-0.3143 °2-0.3389 °2-0.32 °2-0.1118 °2--0.348 °2
S0.098 Å °0.1269 Å °0.0071 Å °-0.4375 Å °-0.1445 Å °-0.1073 Å °0.1318 Å °-0.1839 Å °0.0437 Å °
Refinement TLS groupSelection details: all

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