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- PDB-5hre: The crystal structure of AsfvPolX:DNA3 binary complex -

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Basic information

Entry
Database: PDB / ID: 5hre
TitleThe crystal structure of AsfvPolX:DNA3 binary complex
Components
  • DNA (5'-D(P*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
FORMIC ACID / : / PHOSPHATE ION / 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: 1.75 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _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.ptnr2_symmetry
Revision 1.2Oct 23, 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 (5'-D(P*AP*GP*GP*AP*TP*CP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6566
Polymers23,3662
Non-polymers2914
Water2,198122
1
A: DNA polymerase beta-like protein
B: DNA (5'-D(P*AP*GP*GP*AP*TP*CP*CP*T)-3')
hetero molecules

A: DNA polymerase beta-like protein
B: DNA (5'-D(P*AP*GP*GP*AP*TP*CP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,31312
Polymers46,7314
Non-polymers5828
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5930 Å2
ΔGint-41 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.144, 88.785, 43.349
Angle α, β, γ (deg.)90.00, 94.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / DNA chain , 2 types, 2 molecules AB

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


Mass: 20609.723 Da / Num. of mol.: 1
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(P*AP*GP*GP*AP*TP*CP*CP*T)-3')


Mass: 2755.823 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 126 molecules

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


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.63 Å3/Da / Density % sol: 53.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2M Potassium Formate

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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: 1.75→30 Å / Num. obs: 22860 / % possible obs: 98.7 % / Redundancy: 3.4 % / Net I/σ(I): 26.8

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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: 1.75→26.87 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.857 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23594 1229 5.1 %RANDOM
Rwork0.195 ---
obs0.19709 22860 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.447 Å2
Baniso -1Baniso -2Baniso -3
1--2.87 Å20 Å21.3 Å2
2--2.21 Å20 Å2
3---0.55 Å2
Refinement stepCycle: 1 / Resolution: 1.75→26.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1426 163 14 122 1725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0181644
X-RAY DIFFRACTIONr_bond_other_d0.0010.021598
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.9012245
X-RAY DIFFRACTIONr_angle_other_deg0.7263.0013670
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8125176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.85123.03656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26115291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6571510
X-RAY DIFFRACTIONr_chiral_restr0.0580.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021663
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02361
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_restr1.09933241
X-RAY DIFFRACTIONr_sphericity_free33.867528
X-RAY DIFFRACTIONr_sphericity_bonded6.19253295
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 79 -
Rwork0.229 1665 -
obs--97.21 %
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)
11.59740.25370.27011.64030.04571.4706-0.01680.11160.19610.01110.00910.1035-0.0872-0.07670.00760.06910.0082-0.020.01450.01380.0341-15.391728.14656.0101
22.0008-0.4542-0.71831.95180.61022.0582-0.0407-0.0425-0.31640.2770.03540.12540.2822-0.11780.00530.1735-0.0301-0.03030.01570.02240.0685-14.50216.974514.0948
31.0058-0.0598-0.53460.16650.05280.2907-0.01320.119-0.0252-0.01360.0111-0.03480.0235-0.05840.00220.1096-0.0052-0.0240.0296-0.01370.0213-2.034414.4491-0.3777
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 105
2X-RAY DIFFRACTION2A106 - 174
3X-RAY DIFFRACTION3B2 - 9

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