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- PDB-9emh: KOD-H4 DNA polymerase mutant in a binary complex with DNA:DNA con... -

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Basic information

Entry
Database: PDB / ID: 9emh
TitleKOD-H4 DNA polymerase mutant in a binary complex with DNA:DNA containing two HNA nucleotides
Components
  • DNA (5'-D(*AP*AP*CP*(6HT)P*(6HG)P*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 / HNA
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
IMIDAZOLE / DNA / DNA (> 10) / DNA polymerase
Similarity search - Component
Biological speciesThermococcus kodakarensis KOD1 (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 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*AP*CP*(6HT)P*(6HG)P*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,28210
Polymers98,8653
Non-polymers4177
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7570 Å2
ΔGint-14 kcal/mol
Surface area36500 Å2
Unit cell
Length a, b, c (Å)111.481, 151.624, 67.584
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*AP*CP*(6HT)P*(6HG)P*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')


Mass: 4958.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 44 molecules

#4: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#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.: 37 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.89 Å3/Da / Density % sol: 57.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG 4000, 20% v/v glycerol 0.03 M diethyleneglycol, 0.03 M triethyleneglycol, 0.03 M tetraethyleneglycol, 0.03 M pentaethyleneglycol ethylene glycol, 0.1 M MES/imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.3→46.03 Å / Num. obs: 98077 / % possible obs: 99.6 % / Redundancy: 3.57 % / CC1/2: 0.992 / Net I/σ(I): 3.94
Reflection shellResolution: 2.3→2.44 Å / Num. unique obs: 15751 / CC1/2: 0.119

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→46.03 Å / SU ML: 0.4662 / Cross valid method: FREE R-VALUE / σ(F): 1.19 / Phase error: 33.5868
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2565 2238 3.7 %
Rwork0.2261 58178 -
obs0.2272 60416 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.71 Å2
Refinement stepCycle: LAST / Resolution: 2.7→46.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6200 590 28 37 6855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00247027
X-RAY DIFFRACTIONf_angle_d0.50369587
X-RAY DIFFRACTIONf_chiral_restr0.03951030
X-RAY DIFFRACTIONf_plane_restr0.0041130
X-RAY DIFFRACTIONf_dihedral_angle_d22.5072749
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.760.37841370.40863517X-RAY DIFFRACTION97.44
2.76-2.820.45631440.39463704X-RAY DIFFRACTION99.56
2.82-2.890.39541340.37353628X-RAY DIFFRACTION99.34
2.89-2.970.37831380.3543619X-RAY DIFFRACTION99.29
2.97-3.060.3661420.34733597X-RAY DIFFRACTION99.05
3.06-3.160.38751410.32643632X-RAY DIFFRACTION99.53
3.16-3.270.36861400.29863682X-RAY DIFFRACTION99.48
3.27-3.40.30451370.27123644X-RAY DIFFRACTION99.45
3.4-3.560.2781400.24423652X-RAY DIFFRACTION99.55
3.56-3.740.30571390.26383624X-RAY DIFFRACTION98.84
3.74-3.980.26651420.21423668X-RAY DIFFRACTION99.71
3.98-4.280.19151420.1823617X-RAY DIFFRACTION99.52
4.28-4.710.20121390.16993656X-RAY DIFFRACTION99.87
4.71-5.390.19061400.16833656X-RAY DIFFRACTION99.97
5.4-6.790.19331390.20633648X-RAY DIFFRACTION99.74
6.8-46.030.21191440.16553634X-RAY DIFFRACTION99.11
Refinement TLS params.Method: refined / Origin x: -27.8453290291 Å / Origin y: 21.017216727 Å / Origin z: -18.2544247964 Å
111213212223313233
T0.445068407851 Å20.0507600245296 Å20.00502199102078 Å2-0.580728990721 Å20.0305551881165 Å2--0.513535727756 Å2
L1.10232650025 °20.0521675492705 °2-0.0355321169377 °2-0.823328937876 °20.253254251033 °2--0.448999432127 °2
S0.00774964954723 Å °-0.150307065302 Å °-0.210661690099 Å °0.0284303148624 Å °-0.0898685042161 Å °0.0913711210281 Å °0.0899229482911 Å °0.0281957078237 Å °0.0778560582008 Å °
Refinement TLS groupSelection details: all

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