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- PDB-5hrd: The crystal structure of AsfvPolX:DNA2 binary complex -

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Basic information

Entry
Database: PDB / ID: 5hrd
TitleThe crystal structure of AsfvPolX:DNA2 binary complex
Components
  • DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*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
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: 1.8 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 polymerase beta-like protein
D: DNA polymerase beta-like protein
E: DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*G)-3')
F: DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*G)-3')
G: DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*G)-3')
H: DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,88614
Polymers92,3098
Non-polymers5766
Water5,350297
1
A: DNA polymerase beta-like protein
B: DNA polymerase beta-like protein
E: DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*G)-3')
F: DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4437
Polymers46,1554
Non-polymers2883
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA polymerase beta-like protein
D: DNA polymerase beta-like protein
G: DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*G)-3')
H: DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4437
Polymers46,1554
Non-polymers2883
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.196, 87.485, 87.914
Angle α, β, γ (deg.)90.00, 91.45, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA-1 - 1743 - 178
21LEULEUBB-1 - 1743 - 178
12ARGARGAA-1 - 1733 - 177
22ARGARGCC-1 - 1733 - 177
13ARGARGAA-1 - 1733 - 177
23ARGARGDD-1 - 1733 - 177
14ARGARGBB-1 - 1733 - 177
24ARGARGCC-1 - 1733 - 177
15ARGARGBB-1 - 1733 - 177
25ARGARGDD-1 - 1733 - 177
16LEULEUCC-2 - 1742 - 178
26LEULEUDD-2 - 1742 - 178

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 20609.723 Da / Num. of mol.: 4
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*G)-3')


Mass: 2467.629 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.51 Å3/Da / Density % sol: 50.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M Succinic acid PH 7.0, 15% PGE 3350

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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 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 75045 / % possible obs: 93.5 % / Redundancy: 3.2 % / Net I/σ(I): 20.5

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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: 1.8→29.31 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 10.558 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24456 3936 5 %RANDOM
Rwork0.19646 ---
obs0.1989 75045 93.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.826 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å20 Å2-3.69 Å2
2---2.58 Å2-0 Å2
3---4.24 Å2
Refinement stepCycle: 1 / Resolution: 1.8→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5704 656 30 297 6687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0186564
X-RAY DIFFRACTIONr_bond_other_d0.0050.026420
X-RAY DIFFRACTIONr_angle_refined_deg1.3151.8948974
X-RAY DIFFRACTIONr_angle_other_deg1.424314753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1795702
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.67223.036224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.311151172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5641540
X-RAY DIFFRACTIONr_chiral_restr0.0890.21014
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026646
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021454
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_restr5.42312984
X-RAY DIFFRACTIONr_sphericity_free30.765563
X-RAY DIFFRACTIONr_sphericity_bonded12.385513044
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A115730.08
12B115730.08
21A113450.06
22C113450.06
31A115220.07
32D115220.07
41B114030.06
42C114030.06
51B116700.08
52D116700.08
61C114380.07
62D114380.07
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 278 -
Rwork0.336 5105 -
obs--87.01 %

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