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- PDB-9yd2: Ternary complex of DNA polymerase I from Bacillus stearothermophi... -

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Basic information

Entry
Database: PDB / ID: 9yd2
TitleTernary complex of DNA polymerase I from Bacillus stearothermophilus, large fragment, bound to DNA containing a thymine dimer and dATP
Components
  • DNA (5'-D(*AP*(TTD)P*CP*AP*CP*TP*GP*TP*CP*CP*TP*TP*G)-3')
  • DNA (5'-D(*CP*AP*AP*GP*GP*AP*CP*AP*GP*TP*(DDG))-3')
  • DNA polymerase I
KeywordsREPLICATION / polymerase / complex
Function / homology
Function and homology information


3'-5' exonuclease activity / DNA-templated DNA replication / double-strand break repair / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
: / DNA polymerase I, ribonuclease H-like domain / DNA polymerase 1 / DNA polymerase A / DNA polymerase family A / 3'-5' exonuclease / 3'-5' exonuclease domain / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain ...: / DNA polymerase I, ribonuclease H-like domain / DNA polymerase 1 / DNA polymerase A / DNA polymerase family A / 3'-5' exonuclease / 3'-5' exonuclease domain / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / : / DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.249 Å
AuthorsWu, E.Y. / Walsh, A.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM091487 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01 CA092584 United States
CitationJournal: Biochemistry / Year: 2026
Title: Structural basis for blockage of DNA synthesis by a thymine dimer lesion in a high-fidelity DNA polymerase
Authors: Walsh, A.R. / Beese, L.S. / Wu, E.Y.
History
DepositionSep 20, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase I
B: DNA (5'-D(*CP*AP*AP*GP*GP*AP*CP*AP*GP*TP*(DDG))-3')
C: DNA (5'-D(*AP*(TTD)P*CP*AP*CP*TP*GP*TP*CP*CP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3108
Polymers74,4753
Non-polymers8345
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-59 kcal/mol
Surface area28300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.140, 92.140, 189.690
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase I


Mass: 66260.039 Da / Num. of mol.: 1 / Mutation: D598A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: DPO1, polA / Production host: Escherichia coli (E. coli) / References: UniProt: D9N168, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules BC

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


Mass: 3391.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*(TTD)P*CP*AP*CP*TP*GP*TP*CP*CP*TP*TP*G)-3')


Mass: 4824.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 103 molecules

#4: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.14 Å3/Da / Density % sol: 60.59 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 46% (v/v) saturated ammonium sulfate, 10 mM manganese sulfate (MnSO4), 100 mM 2-(N-morpholino)ethanesulfonic acid (MES), 5% 2-methyl-1,3-propanediol (MPD), 1 mM 2',3'-dideoxyguanosine ...Details: 46% (v/v) saturated ammonium sulfate, 10 mM manganese sulfate (MnSO4), 100 mM 2-(N-morpholino)ethanesulfonic acid (MES), 5% 2-methyl-1,3-propanediol (MPD), 1 mM 2',3'-dideoxyguanosine triphosphate, 5 mM 2'-deoxyadenosine triphosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.249→79.8 Å / Num. obs: 44763 / % possible obs: 99.3 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rrim(I) all: 0.063 / Net I/σ(I): 21.64
Reflection shellResolution: 2.249→2.31 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.42 / Num. unique obs: 3028 / CC1/2: 0.616 / Rrim(I) all: 1 / % possible all: 92.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.249→79.796 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / SU B: 9.217 / SU ML: 0.215 / Cross valid method: FREE R-VALUE / ESU R: 0.258 / ESU R Free: 0.232
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2853 2372 5.299 %
Rwork0.2247 42391 -
all0.228 --
obs-44763 99.229 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 57.896 Å2
Baniso -1Baniso -2Baniso -3
1-0.001 Å20.001 Å20 Å2
2--0.001 Å2-0 Å2
3----0.004 Å2
Refinement stepCycle: LAST / Resolution: 2.249→79.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4651 505 46 98 5300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0125349
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164932
X-RAY DIFFRACTIONr_angle_refined_deg1.9481.8447341
X-RAY DIFFRACTIONr_angle_other_deg0.6421.7611365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0545581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.683544
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.609519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.6110876
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.52310229
X-RAY DIFFRACTIONr_chiral_restr0.090.2828
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025898
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021161
X-RAY DIFFRACTIONr_nbd_refined0.2410.21155
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.24655
X-RAY DIFFRACTIONr_nbtor_refined0.190.22540
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.22822
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2173
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1070.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1980.216
X-RAY DIFFRACTIONr_nbd_other0.1450.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1580.29
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0360.21
X-RAY DIFFRACTIONr_mcbond_it5.8895.3472321
X-RAY DIFFRACTIONr_mcbond_other5.8885.3482321
X-RAY DIFFRACTIONr_mcangle_it8.3199.5942900
X-RAY DIFFRACTIONr_mcangle_other8.3199.5952901
X-RAY DIFFRACTIONr_scbond_it7.1226.483028
X-RAY DIFFRACTIONr_scbond_other7.0776.473016
X-RAY DIFFRACTIONr_scangle_it10.64211.6984438
X-RAY DIFFRACTIONr_scangle_other10.57511.6834421
X-RAY DIFFRACTIONr_lrange_it13.60857.7866153
X-RAY DIFFRACTIONr_lrange_other13.61557.8356144
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.249-2.3080.4041370.4128850.4132810.8990.87992.10610.408
2.308-2.3710.3811760.35429510.35532040.8950.91197.59680.33
2.371-2.440.3832040.32228930.32630970.8940.9281000.289
2.44-2.5150.3391520.30128900.30330420.9170.9381000.262
2.515-2.5970.351310.28328000.28629320.9260.94799.96590.237
2.597-2.6880.3711640.27226850.27828490.9180.9531000.226
2.688-2.7890.3181330.26426380.26627710.9420.9561000.215
2.789-2.9030.3471490.26124830.26626320.9170.9541000.222
2.903-3.0320.3531330.23824010.24425340.920.9631000.204
3.032-3.180.3261210.23723540.24124750.930.9631000.207
3.18-3.3520.3111210.24821950.25123170.9380.96299.95680.225
3.352-3.5540.308980.22621100.2322100.9440.97199.90950.207
3.554-3.7990.3021140.21419660.21820810.9410.97299.9520.196
3.799-4.1030.2741190.20318150.20819350.9550.97399.94830.191
4.103-4.4930.2011130.16816890.1718020.9750.9821000.162
4.493-5.0220.201850.14515600.14816450.9770.9871000.146
5.022-5.7950.256680.213930.20314610.9640.9791000.199
5.795-7.0880.276610.2111880.21412490.9470.9741000.21
7.088-9.9840.241640.1669270.1719910.9620.9821000.188
9.984-79.7960.217290.2315680.2316010.9710.95199.33440.277

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