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

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Basic information

Entry
Database: PDB / ID: 8ilh
TitleThe crystal structure of dG(Se-Sp)-DNA:Pol X product binary complex
Components
  • DNA (5'-D(*CP*GP*GP*AP*TP*CP*C)-3')
  • Repair DNA polymerase X
KeywordsREPLICATION/DNA / DNA polymerase / substrate complex / selenium-modified dNTP / configuration / REPLICATION-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 / 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 / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
Chem-8EB / 2'-DEOXYGUANOSINE-5'-MONOSELENOPHOSPHATE / DNA / Repair DNA polymerase X
Similarity search - Component
Biological speciesAfrican swine fever virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_conn / struct_keywords
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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.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.pdbx_description / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_keywords.pdbx_keywords / _struct_keywords.text

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


Theoretical massNumber of molelcules
Total (without water)93,16828
Polymers90,4848
Non-polymers2,68420
Water10,160564
1
A: Repair DNA polymerase X
B: Repair DNA polymerase X
E: DNA (5'-D(*CP*GP*GP*AP*TP*CP*C)-3')
F: DNA (5'-D(*CP*GP*GP*AP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,62414
Polymers45,2424
Non-polymers1,38210
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-112 kcal/mol
Surface area18530 Å2
MethodPISA
2
C: Repair DNA polymerase X
D: Repair DNA polymerase X
G: DNA (5'-D(*CP*GP*GP*AP*TP*CP*C)-3')
H: DNA (5'-D(*CP*GP*GP*AP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,54414
Polymers45,2424
Non-polymers1,30210
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-117 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.471, 87.280, 87.056
Angle α, β, γ (deg.)90.00, 91.15, 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

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Protein / DNA chain , 2 types, 8 molecules ABCDEFGH

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


Mass: 2098.399 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 584 molecules

#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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-8EB / [[(2R,3S,5R)-5-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-selanyl-phosphoryl] dihydrogen phosphate


Type: DNA linking / Mass: 490.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O9P2Se / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GMS / 2'-DEOXYGUANOSINE-5'-MONOSELENOPHOSPHATE


Type: DNA linking / Mass: 410.182 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O6PSe / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 564 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.53 Å3/Da / Density % sol: 51.47 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: ammonium acetate (0.2 M), HEPES pH 7.2 (0.1 M), 25% 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: Jun 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 51431 / % possible obs: 96.9 % / Redundancy: 5 % / Rmerge(I) obs: 0.078 / Χ2: 0.06 / Net I/σ(I): 8.2 / Num. measured all: 255533
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.1-2.183.40.23745930.907187.2
2.18-2.263.70.22248940.962193
2.26-2.3740.18850800.944196.6
2.37-2.494.10.1851481.01196.9
2.49-2.654.70.16352341.038198.8
2.65-2.855.20.13452211.108199
2.85-3.145.50.10752741.144199.5
3.14-3.595.90.07952811.145199.4
3.59-4.526.50.0653131.004199.7
4.52-306.40.04753930.798199.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 12.226 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2273 2431 5.3 %RANDOM
Rwork0.18069 ---
obs0.18306 43767 87.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.874 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å2-0.04 Å2
2---0.44 Å20 Å2
3---1.17 Å2
Refinement stepCycle: 1 / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5704 622 75 564 6965
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0186566
X-RAY DIFFRACTIONr_bond_other_d0.0050.026421
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.9068965
X-RAY DIFFRACTIONr_angle_other_deg1.327314752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3465702
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61323.036224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.056151172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6181540
X-RAY DIFFRACTIONr_chiral_restr0.0740.21016
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026606
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021442
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_it1.7842.3462820
X-RAY DIFFRACTIONr_mcbond_other1.7832.3462819
X-RAY DIFFRACTIONr_mcangle_it2.1623.5063518
X-RAY DIFFRACTIONr_mcangle_other2.1623.5073519
X-RAY DIFFRACTIONr_scbond_it1.8672.6163746
X-RAY DIFFRACTIONr_scbond_other1.7442.5853706
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.873.7225387
X-RAY DIFFRACTIONr_long_range_B_refined3.4919.6157741
X-RAY DIFFRACTIONr_long_range_B_other3.05119.2057444
X-RAY DIFFRACTIONr_rigid_bond_restr2.228312987
X-RAY DIFFRACTIONr_sphericity_free29.7185139
X-RAY DIFFRACTIONr_sphericity_bonded5.724513247
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A229940.1
12B229940.1
21A224480.08
22C224480.08
31A228160.08
32D228160.08
41B222960.09
42C222960.09
51B228040.1
52D228040.1
61C224220.09
62D224220.09
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 127 -
Rwork0.213 2082 -
obs--57.3 %
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)
10.43040.14950.16911.40140.16880.2974-0.00740.0176-0.0155-0.096-0.0161-0.0494-0.00990.01560.02350.06240.0031-0.00430.00750.00580.011430.2121.853377.661
20.7405-0.47910.52051.9498-0.25460.6156-0.16270.05860.01090.28190.3243-0.0857-0.02140.0398-0.16150.0880.0373-0.06780.1129-0.01320.10941.148821.447298.4658
30.71180.31790.0211.57450.28330.6117-0.0650.08020.0042-0.06530.0181-0.0921-0.0401-0.09650.04690.03190.0021-0.00330.0266-0.0080.020131.357318.612433.5142
40.8643-0.17220.41681.5531-0.40840.4950.00970.13010.07190.20410.06230.04840.01950.0356-0.0720.04350.0131-0.01470.04090.01530.04662.011320.196154.5991
53.1157-0.3927-0.8210.050.10320.21730.05080.15730.3344-0.0010.0083-0.0463-0.0066-0.0467-0.0590.03930.0296-0.02060.0761-0.04640.104613.971916.4387.5087
61.79140.5108-0.48750.148-0.14280.13880.0581-0.24490.09420.0066-0.05040.0223-0.00420.0471-0.00770.08-0.0105-0.0410.1084-0.06220.097619.016216.107786.9576
73.4863-0.465-0.45440.06240.06060.05970.06360.35460.1371-0.0051-0.0472-0.0176-0.0108-0.0527-0.01640.04780.0481-0.00220.1251-0.01470.017315.223814.336243.9479
82.44930.6794-0.99640.1887-0.27640.40540.03520.060.16090.01170.02510.0438-0.0142-0.024-0.06020.09040.0067-0.00330.0493-0.0070.026819.080914.242245.2107
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 174
2X-RAY DIFFRACTION2B1 - 174
3X-RAY DIFFRACTION3C1 - 174
4X-RAY DIFFRACTION4D1 - 174
5X-RAY DIFFRACTION5E1 - 7
6X-RAY DIFFRACTION6F1 - 7
7X-RAY DIFFRACTION7G1 - 7
8X-RAY DIFFRACTION8H1 - 7

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