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- PDB-5hr9: The crystal structure of Se-AsfvPolX(L52/163M mutant) in complex ... -

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Basic information

Entry
Database: PDB / ID: 5hr9
TitleThe crystal structure of Se-AsfvPolX(L52/163M mutant) in complex with 1nt-gap DNA1
Components
  • DNA (5'-D(*GP*GP*AP*CP*AP*AP*CP*GP*GP*GP*AP*CP*AP*AP*C)-3')
  • DNA (5'-D(*GP*TP*TP*GP*TP*CP*C)-3')
  • DNA polymerase beta-like protein
KeywordsTRANSFERASE/DNA / ASFV / PolX / TRANSFERASE-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 / 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 / Repair DNA polymerase X
Similarity search - Component
Biological speciesAfrican swine fever virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsChen, Y.Q. / Zhang, J. / Gan, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Fundation of China31370728 China
CitationJournal: To Be Published
Title: The crystal structure of Se-AsfvPolX(L52/163M mutant) in complex with 1nt-gap DNA1
Authors: Chen, Y.Q. / Zhang, J. / Gan, J.H.
History
DepositionJan 23, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: DNA polymerase beta-like protein
B: DNA polymerase beta-like protein
C: DNA (5'-D(*GP*GP*AP*CP*AP*AP*CP*GP*GP*GP*AP*CP*AP*AP*C)-3')
D: DNA (5'-D(*GP*TP*TP*GP*TP*CP*C)-3')
E: DNA (5'-D(*GP*TP*TP*GP*TP*CP*C)-3')
F: DNA (5'-D(*GP*GP*AP*CP*AP*AP*CP*GP*GP*GP*AP*CP*AP*AP*C)-3')
G: DNA (5'-D(*GP*TP*TP*GP*TP*CP*C)-3')
H: DNA (5'-D(*GP*TP*TP*GP*TP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)59,3588
Polymers59,3588
Non-polymers00
Water1,22568
1
A: DNA polymerase beta-like protein
C: DNA (5'-D(*GP*GP*AP*CP*AP*AP*CP*GP*GP*GP*AP*CP*AP*AP*C)-3')
D: DNA (5'-D(*GP*TP*TP*GP*TP*CP*C)-3')
E: DNA (5'-D(*GP*TP*TP*GP*TP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)29,6794
Polymers29,6794
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-14 kcal/mol
Surface area13570 Å2
MethodPISA
2
B: DNA polymerase beta-like protein
F: DNA (5'-D(*GP*GP*AP*CP*AP*AP*CP*GP*GP*GP*AP*CP*AP*AP*C)-3')
G: DNA (5'-D(*GP*TP*TP*GP*TP*CP*C)-3')
H: DNA (5'-D(*GP*TP*TP*GP*TP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)29,6794
Polymers29,6794
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-11 kcal/mol
Surface area13600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.323, 82.240, 101.416
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 DNA polymerase beta-like protein / PO174L


Mass: 20833.379 Da / Num. of mol.: 2 / Mutation: L52/163M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus / Gene: O174L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0A1E3N6, UniProt: P42494*PLUS
#2: DNA chain DNA (5'-D(*GP*GP*AP*CP*AP*AP*CP*GP*GP*GP*AP*CP*AP*AP*C)-3')


Mass: 4637.040 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain
DNA (5'-D(*GP*TP*TP*GP*TP*CP*C)-3')


Mass: 2104.396 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
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: 2.61 Å3/Da / Density % sol: 52.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 10% w/v PEG 3350, 0.2M L-Proline

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 30053 / % possible obs: 98.2 % / Redundancy: 5.6 % / Net I/σ(I): 15.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.2→29.36 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.914 / SU B: 17.321 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R Free: 0.213 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25596 1609 5.1 %RANDOM
Rwork0.20648 ---
obs0.20906 30053 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.896 Å2
Baniso -1Baniso -2Baniso -3
1-2.48 Å20 Å2-0 Å2
2---6.33 Å20 Å2
3---3.85 Å2
Refinement stepCycle: 1 / Resolution: 2.2→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2858 1174 0 68 4100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0174228
X-RAY DIFFRACTIONr_bond_other_d0.0020.023710
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.725931
X-RAY DIFFRACTIONr_angle_other_deg1.40838569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0575351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.27723.097113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.48615578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1531520
X-RAY DIFFRACTIONr_chiral_restr0.090.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023814
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02930
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.47437938
X-RAY DIFFRACTIONr_sphericity_free63.466516
X-RAY DIFFRACTIONr_sphericity_bonded12.65157799
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 132 -
Rwork0.311 2128 -
obs--96.09 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5486-0.5829-0.24193.3499-0.14850.5397-0.0679-0.0514-0.05090.13380.11990.0283-0.0362-0.0002-0.0520.01610.03330.00820.23370.01270.009433.883827.912832.2211
20.5220.0804-0.56792.9948-0.14232.293-0.08690.0479-0.04540.03270.06760.0235-0.04760.04840.01930.0279-00.00980.2341-0.01450.005141.034846.800221.9898
31.88040.4430.05342.60560.49050.44830.08220.1206-0.0903-0.236-0.01540.0033-0.0005-0.0082-0.06670.04530.0178-0.01620.19830.01460.02032.593438.90118.167
40.7231-0.337-0.07111.75910.01022.1680.0125-0.0923-0.0733-0.0653-0.01890.0359-0.1384-0.07840.00640.0396-0.00720.00090.13560.00810.0076-2.908757.91629.0763
51.4055-2.983-0.81666.6051.97010.75130.00460.1039-0.1685-0.1315-0.21220.4934-0.03520.06480.20770.2245-0.0291-0.06070.3206-0.00490.087736.941316.65198.0428
60.4615-0.7760.3131.90950.17141.2072-0.0358-0.0784-0.0181-0.09170.2274-0.06070.0056-0.0452-0.19160.2541-0.0566-0.05340.3210.00830.041338.232729.921913.7674
70.31341.048-0.791512.93931.58264.0334-0.0487-0.0088-0.1209-0.7323-0.3794-0.04660.0251-0.09360.42810.2036-0.0086-0.04510.3517-0.01250.072642.65084.85641.3926
80.49181.7316-1.21926.4109-4.30453.1235-0.06930.13540.095-0.24940.20510.32920.2245-0.3572-0.13580.0998-0.08520.02860.31750.00010.10981.295729.231142.7505
91.0893-0.10570.09751.8041.10342.75280.0503-0.2541-0.05710.08310.03480.0280.1796-0.0337-0.08510.0846-0.0096-0.00110.21430.05180.02020.844141.153737.0757
101.4266-3.5159-1.71619.61975.71967.63320.01040.3181-0.00740.1495-0.19480.33280.4096-0.16950.18440.4660.0458-0.01220.62120.20360.2006-4.996618.491550.6533
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 105
2X-RAY DIFFRACTION2A106 - 174
3X-RAY DIFFRACTION3B1 - 105
4X-RAY DIFFRACTION4B106 - 174
5X-RAY DIFFRACTION5C1 - 15
6X-RAY DIFFRACTION6D1 - 7
7X-RAY DIFFRACTION7E9 - 15
8X-RAY DIFFRACTION8F1 - 15
9X-RAY DIFFRACTION9G1 - 7
10X-RAY DIFFRACTION10H9 - 15

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