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- PDB-5hrl: The crystal structure of AsfvPolX: 1nt-gap(P) DNA2: dGTP ternary ... -

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Basic information

Entry
Database: PDB / ID: 5hrl
TitleThe crystal structure of AsfvPolX: 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


virion component / base-excision repair / 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 beta thumb / DNA polymerase, thumb domain superfamily ...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 beta thumb / DNA polymerase, thumb domain superfamily / 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: 2.4 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_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
C: 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(*GP*TP*GP*AP*GP*TP*AP*CP*A)-3')
E: DNA (5'-D(P*AP*TP*AP*GP*AP*AP*CP*G)-3')
B: DNA polymerase beta-like protein
F: 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(*GP*TP*GP*AP*GP*TP*AP*CP*A)-3')
H: DNA (5'-D(P*AP*TP*AP*GP*AP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,94015
Polymers62,6148
Non-polymers1,3267
Water81145
1
A: DNA polymerase beta-like protein
C: 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(*GP*TP*GP*AP*GP*TP*AP*CP*A)-3')
E: DNA (5'-D(P*AP*TP*AP*GP*AP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0168
Polymers31,3074
Non-polymers7094
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-21 kcal/mol
Surface area14000 Å2
MethodPISA
2
B: DNA polymerase beta-like protein
F: 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(*GP*TP*GP*AP*GP*TP*AP*CP*A)-3')
H: DNA (5'-D(P*AP*TP*AP*GP*AP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9247
Polymers31,3074
Non-polymers6173
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-23 kcal/mol
Surface area14060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.651, 71.348, 86.922
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYARGARGAA0 - 1734 - 177
21GLYGLYARGARGBE0 - 1734 - 177
12DCDCDCDCCB1 - 181 - 18
22DCDCDCDCFF1 - 181 - 18

NCS ensembles :
ID
1
2

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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: 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

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DNA chain , 3 types, 6 molecules CFDGEH

#2: 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)
#3: 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)
#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, 52 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 3.04 Å3/Da / Density % sol: 59.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M BIS-TRIS pH 5.5, 17% w/v PEG 10000, 0.1 M Ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 28026 / % possible obs: 95.2 % / Redundancy: 5 % / Net I/σ(I): 28.3
Reflection shellResolution: 2.4→2.46 Å

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HR9

5hr9


Resolution: 2.4→28.99 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / SU B: 9.98 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.362 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25713 1482 5 %RANDOM
Rwork0.22779 ---
obs0.22929 28026 95.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.41 Å2
Baniso -1Baniso -2Baniso -3
1--5.69 Å2-0 Å20 Å2
2--5.45 Å20 Å2
3---0.24 Å2
Refinement stepCycle: 1 / Resolution: 2.4→28.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2811 1426 72 45 4354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0164548
X-RAY DIFFRACTIONr_bond_other_d0.0020.023753
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.6986423
X-RAY DIFFRACTIONr_angle_other_deg1.2838653
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3685349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83623.036112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.20115553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2081520
X-RAY DIFFRACTIONr_chiral_restr0.0870.2671
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023969
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02985
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A110770.06
12B110770.06
21C15100.01
22F15100.01
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.467 95 -
Rwork0.39 1923 -
obs--90.21 %

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