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- PDB-5hrf: The crystal structure of AsfvPolX: DNA5: dGTP ternary complex -

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Basic information

Entry
Database: PDB / ID: 5hrf
TitleThe crystal structure of AsfvPolX: DNA5: dGTP ternary complex
Components
  • DNA (5'-D(*CP*AP*GP*GP*AP*TP*CP*CP*T*)-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 / Repair DNA polymerase X / Repair DNA polymerase X
Similarity search - Component
Biological speciesAfrican swine fever virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.25 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 1.1Mar 20, 2024Group: 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_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _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_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

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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(*CP*AP*GP*GP*AP*TP*CP*CP*T*)-3')
D: DNA (5'-D(*CP*AP*GP*GP*AP*TP*CP*CP*T*)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,96710
Polymers46,6514
Non-polymers1,3166
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-45 kcal/mol
Surface area18790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.706, 75.441, 108.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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: 0 - 173 / Label seq-ID: 4 - 177

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

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Components

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Protein / DNA chain , 2 types, 4 molecules ABCD

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


Mass: 20609.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus / Gene: O174L / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A1E3N6, UniProt: P42494*PLUS
#2: DNA chain DNA (5'-D(*CP*AP*GP*GP*AP*TP*CP*CP*T*)-3')


Mass: 2715.799 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 85 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Ammonium citrate pH 7.0 20% w/v PEG 3,350

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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: Jan 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 21028 / % possible obs: 94.2 % / Redundancy: 5.5 % / Net I/σ(I): 27

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.25→28.52 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / SU B: 18.726 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26325 1128 5.1 %RANDOM
Rwork0.21216 ---
obs0.21494 21028 94.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.861 Å2
Baniso -1Baniso -2Baniso -3
1-6.97 Å20 Å2-0 Å2
2---5.53 Å20 Å2
3----1.44 Å2
Refinement stepCycle: 1 / Resolution: 2.25→28.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2763 420 12 79 3274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0183298
X-RAY DIFFRACTIONr_bond_other_d0.0020.023079
X-RAY DIFFRACTIONr_angle_refined_deg1.1641.9064529
X-RAY DIFFRACTIONr_angle_other_deg1.06437043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1755349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.79722.885104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20215521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0051518
X-RAY DIFFRACTIONr_chiral_restr0.0690.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023307
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02725
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_restr1.70936377
X-RAY DIFFRACTIONr_sphericity_free74.507525
X-RAY DIFFRACTIONr_sphericity_bonded10.19156328
Refine LS restraints NCS

Ens-ID: 1 / Number: 10533 / 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: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 97 -
Rwork0.3 1477 -
obs--93.03 %
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)
11.09730.0514-0.39631.7982-0.23431.3441-0.06170.0169-0.1133-0.01010.03170.0877-0.0215-0.020.030.0065-0.00560.02130.27970.01290.21318.634412.64342.5943
21.4274-0.543-0.26921.32170.32082.99950.1045-0.08870.1913-0.1993-0.01970.0092-0.18630.0621-0.08480.0433-0.0399-0.00510.2542-0.01280.217117.825734.66186.6896
32.3061-0.50110.11952.17310.80981.879-0.04210.22010.02770.0013-0.0644-0.3576-0.24820.47160.10660.0407-0.074-0.05110.31750.04190.211552.262921.352230.4832
41.1019-0.32930.58832.50110.8433.6612-0.2403-0.35720.09260.0109-0.0630.1564-0.1052-0.2290.30330.05660.067-0.01460.2651-0.0130.203833.888826.485941.4251
50.7118-0.31390.92840.2171-0.56341.5204-0.0663-0.04590.01770.07480.0539-0.0146-0.1668-0.08210.01240.06140.025-0.05070.3396-0.0560.243731.309820.307917.6176
61.29170.31790.89980.4593-0.67392.7619-0.11040.0978-0.09450.0012-0.0051-0.0644-0.14770.15210.11550.07410.0246-0.00370.2552-0.0010.232433.961121.093719.9149
715.226-9.60037.382914.6696-0.32186.1492-0.2843-0.53960.14720.28260.2884-0.178-0.1073-0.4182-0.00410.13020.01970.02390.1804-0.00250.134927.37224.6132.519
83.2075-1.0737-2.60289.54727.45846.84110.0907-0.0534-0.09020.0402-0.36430.2542-0.0369-0.24610.27360.0919-0.0137-0.04540.2926-0.0490.24839.30515.24733.926
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 105
2X-RAY DIFFRACTION2A106 - 174
3X-RAY DIFFRACTION3B0 - 105
4X-RAY DIFFRACTION4B106 - 174
5X-RAY DIFFRACTION5C1 - 9
6X-RAY DIFFRACTION6D1 - 9
7X-RAY DIFFRACTION7A202
8X-RAY DIFFRACTION8B203

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