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- PDB-8s8t: KOD-H4 DNA polymerase mutant in a binary complex with DNA/DNA -

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Basic information

Entry
Database: PDB / ID: 8s8t
TitleKOD-H4 DNA polymerase mutant in a binary complex with DNA/DNA
Components
  • DNA (5'-D(*AP*CP*TP*GP*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
  • DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*CP*A)-3')
  • DNA polymerase
KeywordsTRANSFERASE / Polymerase / XNA / modified nucleotides / Reverse transcriptase
Function / homology
Function and homology information


DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
: / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family ...: / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA polymerase
Similarity search - Component
Biological speciesThermococcus kodakarensis KOD1 (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGutfreund, C. / Betz, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: To Be Published
Title: Crystallographic Insights into a Mutant Archaeal B-Family Polymerase processing HNA
Authors: Gutfreund, C. / Betz, K.
History
DepositionMar 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2025Provider: 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
P: DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*CP*A)-3')
T: DNA (5'-D(*AP*CP*TP*GP*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,11310
Polymers98,8373
Non-polymers2767
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-63 kcal/mol
Surface area36560 Å2
Unit cell
Length a, b, c (Å)111.552, 149.297, 66.216
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase


Mass: 89976.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis KOD1 (archaea)
Production host: Escherichia coli (E. coli) / References: UniProt: D0VWU9, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules PT

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


Mass: 3930.578 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*CP*TP*GP*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')


Mass: 4930.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 43 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.79 Å3/Da / Density % sol: 55.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 10% (w/v) Polyethylene glycol 8,000, 100 mM TRIS; pH 8.0 10% (v/v) Glycerol, 1 mM Tris(2-carboxyethyl)phosphine hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.25→49.52 Å / Num. obs: 100438 / % possible obs: 99.1 % / Redundancy: 3.17 % / CC1/2: 0.989 / Net I/σ(I): 3.95
Reflection shellResolution: 2.25→2.39 Å / Num. unique obs: 16062 / CC1/2: 0.115

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→45.45 Å / SU ML: 0.4416 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.5439
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2424 1599 3.78 %
Rwork0.1852 40753 -
obs0.1873 42352 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.1 Å2
Refinement stepCycle: LAST / Resolution: 3→45.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6200 567 15 36 6818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00356979
X-RAY DIFFRACTIONf_angle_d0.62949527
X-RAY DIFFRACTIONf_chiral_restr0.04241027
X-RAY DIFFRACTIONf_plane_restr0.00561123
X-RAY DIFFRACTIONf_dihedral_angle_d18.51072737
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.10.41361390.30973610X-RAY DIFFRACTION96.87
3.1-3.210.32981470.29263702X-RAY DIFFRACTION99.33
3.21-3.340.30481420.24083726X-RAY DIFFRACTION99.33
3.34-3.490.28911470.22743738X-RAY DIFFRACTION99.18
3.49-3.670.26931420.20893693X-RAY DIFFRACTION99.1
3.67-3.90.25131470.19023706X-RAY DIFFRACTION99.33
3.9-4.20.22311460.1613715X-RAY DIFFRACTION99.54
4.2-4.630.19261440.14483720X-RAY DIFFRACTION99.43
4.63-5.290.21921480.15233722X-RAY DIFFRACTION99.54
5.29-6.670.22731450.1763736X-RAY DIFFRACTION99.46
6.67-45.450.18921520.14453685X-RAY DIFFRACTION98.89
Refinement TLS params.Method: refined / Origin x: -27.8678034705 Å / Origin y: 20.5706227609 Å / Origin z: -14.9808378484 Å
111213212223313233
T0.361693265539 Å2-0.0363614528859 Å20.00454996645997 Å2-0.395727422922 Å20.0146294308455 Å2--0.409847199941 Å2
L1.02378787938 °20.14391240301 °2-0.168547732736 °2-0.859080173538 °2-0.302610680654 °2--0.518782064759 °2
S0.0150200481508 Å °0.0182144278001 Å °-0.122726919526 Å °-0.0209527192429 Å °-0.124644219249 Å °-0.215901671493 Å °0.0745966398585 Å °0.0173819712562 Å °0.119120186249 Å °
Refinement TLS groupSelection details: all

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