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- PDB-5hrh: The crystal structure of AsfvPolX(H115F/R127A mutant): 1nt-gap(P)... -

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Basic information

Entry
Database: PDB / ID: 5hrh
TitleThe crystal structure of AsfvPolX(H115F/R127A mutant): 1nt-gap(P) DNA2:dGTP ternary complex
Components
  • DNA (5'-D(*CP*GP*TP*TP*CP*TP*AP*TP*GP*TP*GP*TP*AP*CP*TP*CP*AP*C)-3')
  • DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*A*)-3')
  • DNA (5'-D(P*AP*TP*AP*GP*AP*AP*CP*G)-3')
  • DNA polymerase beta-like protein
KeywordsTRANSFERASE/DNA / ASFV / PolX / 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
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / : / 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: 3 Å
AuthorsChen, Y.Q. / Zhang, J. / Gan, J.H.
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 1.1Jan 25, 2017Group: Source and taxonomy
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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
C: DNA (5'-D(*CP*GP*TP*TP*CP*TP*AP*TP*GP*TP*GP*TP*AP*CP*TP*CP*AP*C)-3')
D: DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*A*)-3')
E: DNA (5'-D(P*AP*TP*AP*GP*AP*AP*CP*G)-3')
B: DNA polymerase beta-like protein
F: DNA (5'-D(*CP*GP*TP*TP*CP*TP*AP*TP*GP*TP*GP*TP*AP*CP*TP*CP*AP*C)-3')
G: DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*A*)-3')
H: DNA (5'-D(P*AP*TP*AP*GP*AP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,69314
Polymers62,4598
Non-polymers1,2346
Water362
1
A: DNA polymerase beta-like protein
C: DNA (5'-D(*CP*GP*TP*TP*CP*TP*AP*TP*GP*TP*GP*TP*AP*CP*TP*CP*AP*C)-3')
D: DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*A*)-3')
E: DNA (5'-D(P*AP*TP*AP*GP*AP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8477
Polymers31,2304
Non-polymers6173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-26 kcal/mol
Surface area13630 Å2
MethodPISA
2
B: DNA polymerase beta-like protein
F: DNA (5'-D(*CP*GP*TP*TP*CP*TP*AP*TP*GP*TP*GP*TP*AP*CP*TP*CP*AP*C)-3')
G: DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*A*)-3')
H: DNA (5'-D(P*AP*TP*AP*GP*AP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8477
Polymers31,2304
Non-polymers6173
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-31 kcal/mol
Surface area14110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.500, 70.030, 86.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA polymerase beta-like protein / PO174L / PolX


Mass: 20532.635 Da / Num. of mol.: 2 / Mutation: H115F, R127A
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

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DNA chain , 3 types, 6 molecules CFDGEH

#2: DNA chain DNA (5'-D(*CP*GP*TP*TP*CP*TP*AP*TP*GP*TP*GP*TP*AP*CP*TP*CP*AP*C)-3')


Mass: 5457.539 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*A*)-3')


Mass: 2779.848 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*AP*TP*AP*GP*AP*AP*CP*G)-3')


Mass: 2459.656 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 8 molecules

#5: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Deoxyguanosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#6: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.98 Å3/Da / Density % sol: 58.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% (w/v) PEG 3350, 100 mM HEPES pH 7.5, 200 mM Sodium chloride

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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: Jul 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 15302 / % possible obs: 99.1 % / Redundancy: 11 % / Net I/σ(I): 16.7
Reflection shellResolution: 3→3.18 Å

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3→29.986 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2727 817 5.34 %
Rwork0.2316 --
obs0.2338 15302 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→29.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2702 1426 66 2 4196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114414
X-RAY DIFFRACTIONf_angle_d1.4356299
X-RAY DIFFRACTIONf_dihedral_angle_d22.5022353
X-RAY DIFFRACTIONf_chiral_restr0.07736
X-RAY DIFFRACTIONf_plane_restr0.008537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.18780.39641380.32642320X-RAY DIFFRACTION95
3.1878-3.43360.40651340.28662291X-RAY DIFFRACTION95
3.4336-3.77850.32781150.27862432X-RAY DIFFRACTION98
3.7785-4.32390.29211320.23622427X-RAY DIFFRACTION98
4.3239-5.44230.26991440.222460X-RAY DIFFRACTION98
5.4423-29.98780.20541540.19012555X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 151.6932 Å / Origin y: 70.7065 Å / Origin z: 107.6381 Å
111213212223313233
T0.4953 Å2-0.2022 Å2-0.0907 Å2-0.7045 Å20.0572 Å2--0.444 Å2
L2.0131 °2-1.7117 °2-0.4968 °2-3.098 °20.0264 °2--0.8497 °2
S0.1239 Å °0.1856 Å °0.0975 Å °0.0552 Å °-0.2619 Å °-0.219 Å °0.0168 Å °0.0374 Å °0.1299 Å °
Refinement TLS groupSelection details: all

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