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- PDB-8ilg: The crystal structure of dG-DNA:Pol X product binary complex -

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Basic information

Entry
Database: PDB / ID: 8ilg
TitleThe crystal structure of dG-DNA:Pol X product binary complex
Components
  • DNA (5'-D(*CP*GP*GP*AP*TP*CP*CP*G)-3')
  • Repair DNA polymerase X
KeywordsREPLICATION/DNA / DNA polymerase / substrate complex / selenium-modified dNTP / configuration / REPLICATION-DNA complex
Function / homology
Function and homology information


double-strand break repair via nonhomologous end joining / virion component / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / metal ion binding
Similarity search - Function
Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase 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 / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
FORMIC ACID / : / DNA / Repair DNA polymerase X
Similarity search - Component
Biological speciesAfrican swine fever virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.805 Å
AuthorsQin, T. / Gan, J.H. / Huang, Z.
Funding support China, 4items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2303700 China
National Natural Science Foundation of China (NSFC)22107079 China
National Natural Science Foundation of China (NSFC)22077089 China
Ministry of Education (MoE, China)2020M673205 China
CitationJournal: Int J Mol Sci / Year: 2023
Title: Structural Insight into Polymerase Mechanism via a Chiral Center Generated with a Single Selenium Atom.
Authors: Qin, T. / Hu, B. / Zhao, Q. / Wang, Y. / Wang, S. / Luo, D. / Lyu, J. / Chen, Y. / Gan, J. / Huang, Z.
History
DepositionMar 3, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Repair DNA polymerase X
D: DNA (5'-D(*CP*GP*GP*AP*TP*CP*CP*G)-3')
E: DNA (5'-D(*CP*GP*GP*AP*TP*CP*CP*G)-3')
B: Repair DNA polymerase X
C: DNA (5'-D(*CP*GP*GP*AP*TP*CP*CP*G)-3')
F: DNA (5'-D(*CP*GP*GP*AP*TP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,98610
Polymers50,7846
Non-polymers2024
Water9,674537
1
A: Repair DNA polymerase X
D: DNA (5'-D(*CP*GP*GP*AP*TP*CP*CP*G)-3')
E: DNA (5'-D(*CP*GP*GP*AP*TP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4935
Polymers25,3923
Non-polymers1012
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-13 kcal/mol
Surface area10760 Å2
MethodPISA
2
B: Repair DNA polymerase X
C: DNA (5'-D(*CP*GP*GP*AP*TP*CP*CP*G)-3')
F: DNA (5'-D(*CP*GP*GP*AP*TP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4935
Polymers25,3923
Non-polymers1012
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-14 kcal/mol
Surface area10870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.033, 81.422, 92.594
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Repair DNA polymerase X / Pol X / AsfvPolX


Mass: 20536.668 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)
Gene: Ba71V-97, O174L / Production host: Escherichia coli (E. coli) / References: UniProt: P42494, DNA-directed DNA polymerase
#2: DNA chain
DNA (5'-D(*CP*GP*GP*AP*TP*CP*CP*G)-3')


Mass: 2427.605 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 52.06 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: Potassium Formate (0.2 M), 16% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 84882 / % possible obs: 91.6 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.136 / Χ2: 0.111 / Net I/σ(I): 6.1 / Num. measured all: 209940
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.8-1.861.80.37174330.549180
1.86-1.9420.34178210.647184.6
1.94-2.0320.27279790.736186.3
2.03-2.132.10.2282730.922189.1
2.13-2.272.30.19983821.131190.8
2.27-2.442.40.16386861.218194
2.44-2.692.60.14388661.682195.7
2.69-3.082.80.1290192.203197.3
3.08-3.883.20.11291983.917199.3
3.88-303.30.08392253.878199.5

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
REFMAC5.7.0029refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.805→28.861 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2551 2428 5.13 %
Rwork0.2216 --
obs0.2234 47365 97.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.805→28.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2825 644 8 537 4014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083601
X-RAY DIFFRACTIONf_angle_d0.964982
X-RAY DIFFRACTIONf_dihedral_angle_d17.6992072
X-RAY DIFFRACTIONf_chiral_restr0.059580
X-RAY DIFFRACTIONf_plane_restr0.006505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.805-1.84160.31111300.30292426X-RAY DIFFRACTION90
1.8416-1.88160.35371500.29452515X-RAY DIFFRACTION95
1.8816-1.92540.32991200.28132596X-RAY DIFFRACTION96
1.9254-1.97350.23881370.26022553X-RAY DIFFRACTION95
1.9735-2.02690.29251490.23962573X-RAY DIFFRACTION96
2.0269-2.08650.26411460.2392586X-RAY DIFFRACTION97
2.0865-2.15380.26271280.21472643X-RAY DIFFRACTION97
2.1538-2.23080.28351590.21522577X-RAY DIFFRACTION97
2.2308-2.32010.23941440.21392661X-RAY DIFFRACTION98
2.3201-2.42560.26431600.21512629X-RAY DIFFRACTION99
2.4256-2.55340.26171370.21222680X-RAY DIFFRACTION99
2.5534-2.71330.29221250.22522699X-RAY DIFFRACTION99
2.7133-2.92260.24391460.23032694X-RAY DIFFRACTION99
2.9226-3.21640.26121490.22222723X-RAY DIFFRACTION99
3.2164-3.6810.23921560.21142707X-RAY DIFFRACTION99
3.681-4.63450.19981470.19012792X-RAY DIFFRACTION100
4.6345-28.860.26571450.2152883X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 87.1167 Å / Origin y: 30.2348 Å / Origin z: 115.6841 Å
111213212223313233
T0.1797 Å20.0061 Å2-0.0128 Å2-0.1761 Å20.0119 Å2--0.1145 Å2
L0.7783 °20.1393 °20.1113 °2-0.4518 °2-0.0091 °2--0.1544 °2
S-0.0286 Å °0.0376 Å °0.0781 Å °0.0202 Å °0.0194 Å °0.0023 Å °-0.0198 Å °0.0363 Å °0.0206 Å °
Refinement TLS groupSelection details: all

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