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- PDB-8ile: The crystal structure of dGTPalphaSe-Rp:DNApre-II:Pol X substrate... -

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Basic information

Entry
Database: PDB / ID: 8ile
TitleThe crystal structure of dGTPalphaSe-Rp:DNApre-II:Pol X substrate ternary complex
Components
  • DNA (5'-D(*CP*TP*GP*GP*AP*TP*CP*CP*A)-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
Chem-7Q6 / : / DNA / Repair DNA polymerase X
Similarity search - Component
Biological speciesAfrican swine fever virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 1.1Nov 13, 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
A: Repair DNA polymerase X
B: Repair DNA polymerase X
E: DNA (5'-D(*CP*TP*GP*GP*AP*TP*CP*CP*A)-3')
G: DNA (5'-D(*CP*TP*GP*GP*AP*TP*CP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,72310
Polymers46,3634
Non-polymers1,3606
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.481, 77.382, 111.353
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Repair DNA polymerase X / Pol X / AsfvPolX


Mass: 20465.592 Da / Num. of mol.: 2
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
#2: DNA chain DNA (5'-D(*CP*TP*GP*GP*AP*TP*CP*CP*A)-3')


Mass: 2715.799 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-7Q6 / [[(2R,3S,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-selanyl-phosphoryl] phosphono hydrogen phosphate


Mass: 570.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3Se / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.8 Å3/Da / Density % sol: 56.05 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M L-proline, HEPES pH 8.6 (0.1 M),10% PEG 3350

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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: Nov 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 10889 / % possible obs: 99.9 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.117 / Χ2: 0.216 / Net I/σ(I): 7.8 / Num. measured all: 138097
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
3-3.1112.81.22510631.0431100
3.11-3.2313.40.74210741.061199.8
3.23-3.3813.30.42910631.0091100
3.38-3.5613.10.34510601.2541100
3.56-3.7812.80.22810691.209199.9
3.78-4.0711.30.14610851.131199.6
4.07-4.4812.40.08510780.933199.9
4.48-5.1213.30.06511030.849199.9
5.12-6.4412.80.0611140.943199.8
6.44-3011.60.09811802.246199.7

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Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
REFMAC5.7.0029refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→29.74 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.857 / SU B: 38.321 / SU ML: 0.323 / Cross valid method: THROUGHOUT / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28371 515 5.2 %RANDOM
Rwork0.22045 ---
obs0.22365 9335 91.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.522 Å2
Baniso -1Baniso -2Baniso -3
1--23.49 Å2-0 Å2-0 Å2
2---0.12 Å20 Å2
3---23.61 Å2
Refinement stepCycle: 1 / Resolution: 3→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2650 358 66 4 3078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0183163
X-RAY DIFFRACTIONr_bond_other_d0.0030.022893
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.8934374
X-RAY DIFFRACTIONr_angle_other_deg1.07636603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0865343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.8323.13199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.05615467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6861517
X-RAY DIFFRACTIONr_chiral_restr0.0680.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023217
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02690
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_it3.2513.7311381
X-RAY DIFFRACTIONr_mcbond_other3.2513.731380
X-RAY DIFFRACTIONr_mcangle_it4.5895.5871721
X-RAY DIFFRACTIONr_mcangle_other4.5875.5881722
X-RAY DIFFRACTIONr_scbond_it3.333.491782
X-RAY DIFFRACTIONr_scbond_other3.3293.4861779
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4595.1942652
X-RAY DIFFRACTIONr_long_range_B_refined6.03328.6913480
X-RAY DIFFRACTIONr_long_range_B_other6.01728.6923479
X-RAY DIFFRACTIONr_rigid_bond_restr3.05836056
X-RAY DIFFRACTIONr_sphericity_free70.62551
X-RAY DIFFRACTIONr_sphericity_bonded12.95455970
Refine LS restraints NCS

Ens-ID: 1 / Number: 18582 / 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: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 23 -
Rwork0.256 408 -
obs--55.04 %
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)
16.33390.3264-1.70032.63410.21444.9742-0.0970.3769-0.4594-0.6808-0.1995-0.2150.566-0.02770.29650.4541-0.06770.07360.14820.00650.059415.1779-23.0868-35.3955
23.76190.85191.33153.47621.71153.1106-0.19-0.35910.0248-0.046-0.1640.3934-0.2119-0.11770.3540.03520.0289-0.00130.0510.00310.0723-11.8307-22.1505-4.6275
36.6694-0.9069-5.02990.12360.6843.8350.2040.1720.1765-0.031-0.0391-0.0206-0.2829-0.0948-0.16490.3688-0.08480.02920.22420.01120.1191.3854-20.6081-17.7467
45.93991.3369-4.85270.3985-1.45747.01-0.24730.11650.1929-0.06970.150.0321-0.1617-0.07230.09720.1715-0.1143-0.00890.25260.04990.13153.9596-21.2511-20.2356
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 174
2X-RAY DIFFRACTION2B1 - 174
3X-RAY DIFFRACTION3E0 - 8
4X-RAY DIFFRACTION4G2 - 10

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