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- PDB-8ili: The crystal structure of dG(Se-Rp)-DNA:Pol X product binary complex -

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Basic information

Entry
Database: PDB / ID: 8ili
TitleThe crystal structure of dG(Se-Rp)-DNA:Pol X product binary complex
Components
  • DNA (5'-D(*CP*GP*GP*AP*TP*CP*CP*(7S8))-3')
  • Repair DNA polymerase X
KeywordsREPLICATION/DNA / DNA polymerase / substrate complex / selenium-modified dNTP / configuration / REPLICATION-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 / 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 / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
DNA / Repair DNA polymerase X
Similarity search - Component
Biological speciesAfrican swine fever virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsQin, T. / Gan, J.H. / Huang, Z.
Funding support China, 4items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2303700 China
National Natural Science Foundation of China (NSFC)22107079 China
National Natural Science Foundation of China (NSFC)22077089 China
Ministry of Education (MoE, China)2020M673205 China
CitationJournal: Int J Mol Sci / Year: 2023
Title: Structural Insight into Polymerase Mechanism via a Chiral Center Generated with a Single Selenium Atom.
Authors: Qin, T. / Hu, B. / Zhao, Q. / Wang, Y. / Wang, S. / Luo, D. / Lyu, J. / Chen, Y. / Gan, J. / Huang, Z.
History
DepositionMar 3, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 2.0Jan 17, 2024Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_instance_feature / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _ndb_struct_na_base_pair.i_label_comp_id / _ndb_struct_na_base_pair.j_label_comp_id / _ndb_struct_na_base_pair.pair_name / _ndb_struct_na_base_pair_step.i_label_comp_id_2 / _ndb_struct_na_base_pair_step.j_label_comp_id_1 / _ndb_struct_na_base_pair_step.step_name / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id
Revision 2.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: DNA (5'-D(*CP*GP*GP*AP*TP*CP*CP*(7S8))-3')
F: DNA (5'-D(*CP*GP*GP*AP*TP*CP*CP*(7S8))-3')
G: DNA (5'-D(*CP*GP*GP*AP*TP*CP*CP*(7S8))-3')
H: DNA (5'-D(*CP*GP*GP*AP*TP*CP*CP*(7S8))-3')
A: Repair DNA polymerase X
B: Repair DNA polymerase X
C: Repair DNA polymerase X
D: Repair DNA polymerase X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,01624
Polymers92,0538
Non-polymers96316
Water12,809711
1
E: DNA (5'-D(*CP*GP*GP*AP*TP*CP*CP*(7S8))-3')
F: DNA (5'-D(*CP*GP*GP*AP*TP*CP*CP*(7S8))-3')
A: Repair DNA polymerase X
B: Repair DNA polymerase X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,60413
Polymers46,0264
Non-polymers5789
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-126 kcal/mol
Surface area18610 Å2
MethodPISA
2
G: DNA (5'-D(*CP*GP*GP*AP*TP*CP*CP*(7S8))-3')
H: DNA (5'-D(*CP*GP*GP*AP*TP*CP*CP*(7S8))-3')
C: Repair DNA polymerase X
D: Repair DNA polymerase X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,41211
Polymers46,0264
Non-polymers3857
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-98 kcal/mol
Surface area18810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.420, 87.344, 87.480
Angle α, β, γ (deg.)90.00, 91.16, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
/ NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: DNA chain
DNA (5'-D(*CP*GP*GP*AP*TP*CP*CP*(7S8))-3')


Mass: 2490.566 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein
Repair DNA polymerase X / Pol X / AsfvPolX


Mass: 20522.643 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus (strain Badajoz 1971 Vero-adapted)
Gene: Ba71V-97, O174L / Production host: Escherichia coli (E. coli) / References: UniProt: P42494, DNA-directed DNA polymerase
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 711 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: ammonium sulfate (0.2 M), Bis-Tris pH 6.5 (0.1 M), 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 69608 / % possible obs: 97.1 % / Redundancy: 5 % / Rmerge(I) obs: 0.06 / Χ2: 0.046 / Net I/σ(I): 9.6 / Num. measured all: 346977
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.9-1.973.40.26461910.872187.4
1.97-2.053.50.23466210.922192.5
2.05-2.144.10.21369550.998197.3
2.14-2.254.50.18270181.051198.3
2.25-2.394.70.14770501.105198.7
2.39-2.584.90.12170601.174198.7
2.58-2.845.60.09271081.167199.4
2.84-3.255.70.06871551.188199.4
3.25-4.096.70.04471781.028199.8
4.09-306.50.03772720.921199.5

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.7.0029refinement
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.919 / SU B: 3.713 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24293 3219 5 %RANDOM
Rwork0.21517 ---
obs0.21657 61518 90.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.102 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0 Å2-0.25 Å2
2---0.37 Å20 Å2
3---0.63 Å2
Refinement stepCycle: 1 / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5673 644 48 711 7076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0186533
X-RAY DIFFRACTIONr_bond_other_d0.0030.026356
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.8968930
X-RAY DIFFRACTIONr_angle_other_deg1.096314596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1625705
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.95722.941221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.267151146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0561540
X-RAY DIFFRACTIONr_chiral_restr0.0660.21015
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026616
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021452
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_it0.9232.3052826
X-RAY DIFFRACTIONr_mcbond_other0.9232.3052825
X-RAY DIFFRACTIONr_mcangle_it1.653.4493526
X-RAY DIFFRACTIONr_mcangle_other1.653.4493527
X-RAY DIFFRACTIONr_scbond_it0.7882.2513707
X-RAY DIFFRACTIONr_scbond_other0.7822.2233675
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3573.2815355
X-RAY DIFFRACTIONr_long_range_B_refined5.23218.3257883
X-RAY DIFFRACTIONr_long_range_B_other4.51617.6677439
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)
11A225700.07
12B225700.07
21A224660.06
22C224660.06
31A225120.06
32D225120.06
41B221280.05
42C221280.05
51B224160.05
52D224160.05
61C225000.05
62D225000.05
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 91 -
Rwork0.253 2851 -
obs--55.85 %

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