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- PDB-5hrg: The crystal structure of AsfvPolX(D51N mutant):DNA4 binary complex -

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Basic information

Entry
Database: PDB / ID: 5hrg
TitleThe crystal structure of AsfvPolX(D51N mutant):DNA4 binary complex
Components
  • DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3')
  • DNA polymerase beta-like protein
KeywordsTRANSFERASE/DNA / ASFV / PolX / TRANSFERASE-DNA complex
Function / homology
Function and homology information


virion component / 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, 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 / 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 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_ncs_dom_lim
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 / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 6, 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
C: DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3')
D: DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,66311
Polymers46,0734
Non-polymers5907
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-89 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.060, 51.170, 55.540
Angle α, β, γ (deg.)68.35, 86.25, 88.20
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: -1 - 173 / Label seq-ID: 3 - 177

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 20608.738 Da / Num. of mol.: 2 / Mutation: D51N
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*CP*GP*AP*TP*CP*GP*C)-3')


Mass: 2427.605 Da / Num. of mol.: 2 / 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
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES pH 7.5, 20% (w/v) PEG 8000, 200mM Ammonium sulfate 10% (v/v) 2-Propanol

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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: Mar 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 27077 / % possible obs: 93.8 % / Redundancy: 2.9 % / Net I/σ(I): 6.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HR9

5hr9


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.916 / SU B: 11.233 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23893 1443 5.1 %RANDOM
Rwork0.19072 ---
obs0.19319 27077 93.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.146 Å2
Baniso -1Baniso -2Baniso -3
1-2.58 Å21.1 Å21.34 Å2
2---2.69 Å2-0.07 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2857 322 27 161 3367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0183295
X-RAY DIFFRACTIONr_bond_other_d0.0020.023205
X-RAY DIFFRACTIONr_angle_refined_deg1.0851.94493
X-RAY DIFFRACTIONr_angle_other_deg0.82237362
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0985352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.35723.158114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2615583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1011520
X-RAY DIFFRACTIONr_chiral_restr0.060.2509
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023336
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02732
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_restr2.39436500
X-RAY DIFFRACTIONr_sphericity_free38.544535
X-RAY DIFFRACTIONr_sphericity_bonded6.37256537
Refine LS restraints NCS

Ens-ID: 1 / Number: 11428 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 116 -
Rwork0.265 2015 -
obs--94.42 %
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)
12.29240.6729-1.01781.8841-0.2441.84780.033-0.04290.17120.06360.04370.0281-0.13080.0184-0.07660.021-0.0279-0.00570.0990.02050.019313.8214-23.584242.9712
21.91350.55470.49770.8640.59031.386-0.03080.0677-0.1828-0.06950.1471-0.18990.05530.1119-0.11630.023-0.0260.0180.14440.00250.060918.5364-42.393331.1812
32.64250.2807-1.30961.52320.09422.4837-0.10230.00240.07640.02040.06680.0870.05870.07070.03550.0099-0.0231-0.00850.11880.03950.0185-2.2192-7.750518.4747
42.739-0.8148-1.02013.14290.92183.2857-0.17110.4867-0.285-0.0169-0.20360.51790.5406-0.40760.37470.1305-0.12980.03040.2312-0.05590.1078-11.6701-26.32599.6714
51.3632-1.45431.12321.5752-1.26151.0971-0.00080.13160.0634-0.0378-0.1522-0.10370.10510.16940.15290.2074-0.02830.02030.19440.0370.10014.8923-26.884722.1582
60.2429-0.33050.71170.5661-1.12492.297-0.0472-0.0673-0.03240.14250.07120.0071-0.2699-0.1351-0.0240.1303-0.03520.00560.17760.02120.06433.6432-28.716625.5968
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 105
2X-RAY DIFFRACTION2A106 - 174
3X-RAY DIFFRACTION3B-2 - 105
4X-RAY DIFFRACTION4B106 - 174
5X-RAY DIFFRACTION5C1 - 8
6X-RAY DIFFRACTION6D1 - 8

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