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- PDB-5hrk: The crystal structure of AsfvPolX(H115F mutant): 1nt-gap(P) DNA2:... -

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Basic information

Entry
Database: PDB / ID: 5hrk
TitleThe crystal structure of AsfvPolX(H115F 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


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
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 / MOLECULAR REPLACEMENT / Resolution: 2.9 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 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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


Theoretical massNumber of molelcules
Total (without water)64,25018
Polymers62,6328
Non-polymers1,61810
Water362
1
A: DNA polymerase beta-like protein
F: DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*A)-3')
H: 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(P*AP*TP*AP*GP*AP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1259
Polymers31,3164
Non-polymers8095
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-55 kcal/mol
Surface area14310 Å2
MethodPISA
2
B: DNA polymerase beta-like protein
C: DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*A)-3')
E: 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(P*AP*TP*AP*GP*AP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1259
Polymers31,3164
Non-polymers8095
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-52 kcal/mol
Surface area13980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.726, 87.196, 82.616
Angle α, β, γ (deg.)90.00, 97.59, 90.00
Int Tables number5
Space group name H-MC121

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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: 20618.750 Da / Num. of mol.: 2 / Mutation: H115F
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 FCHEGD

#2: 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)
#3: 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)
#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 , 4 types, 12 molecules

#5: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 20% (w/v) PEG 3350 200 mM Sodium iodide

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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 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 16476 / % possible obs: 99 % / Redundancy: 4.3 % / Net I/σ(I): 22.9

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HR9

2hr9


Resolution: 2.9→28.027 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 37.85
RfactorNum. reflection% reflection
Rfree0.2725 840 5.1 %
Rwork0.233 --
obs0.2351 16476 97.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→28.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2653 1488 24 2 4167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124381
X-RAY DIFFRACTIONf_angle_d1.546262
X-RAY DIFFRACTIONf_dihedral_angle_d23.3652328
X-RAY DIFFRACTIONf_chiral_restr0.089728
X-RAY DIFFRACTIONf_plane_restr0.011533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8957-3.0770.39681360.34252550X-RAY DIFFRACTION96
3.077-3.31420.3761240.30962567X-RAY DIFFRACTION96
3.3142-3.64710.31211540.26482569X-RAY DIFFRACTION97
3.6471-4.17330.33071310.2582612X-RAY DIFFRACTION99
4.1733-5.25230.25991310.22472668X-RAY DIFFRACTION100
5.2523-28.02810.21431640.18512670X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -158.775 Å / Origin y: -104.2499 Å / Origin z: -180.1197 Å
111213212223313233
T0.4893 Å2-0.0136 Å2-0.1006 Å2-0.3861 Å20.015 Å2--0.5982 Å2
L1.405 °20.0783 °20.3712 °2-0.6324 °20.5239 °2--3.7218 °2
S0.1041 Å °0.1556 Å °-0.138 Å °0.0088 Å °0.0512 Å °-0.0093 Å °0.0954 Å °-0.1505 Å °-0.1238 Å °
Refinement TLS groupSelection details: all

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