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- PDB-9en0: KOD-H4 DNA polymerase mutant in a unproductive binary complex wit... -

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Basic information

Entry
Database: PDB / ID: 9en0
TitleKOD-H4 DNA polymerase mutant in a unproductive binary complex with DNA:DNA containing six HNA nucleotides
Components
  • DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*CP*A)-3')
  • DNA (5'-D(P*AP*CP*(6HT)P*(6HG)P*(6HT)P*(6HG)P*(6HG)P*(6HC)P*CP*GP*TP*GP*GP*TP*C)-3')
  • DNA polymerase
KeywordsTRANSFERASE / Polymerase / XNA / modified nucleotides / Reverse transcriptase / AtNA
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: 2.51 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 12, 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
T: DNA (5'-D(P*AP*CP*(6HT)P*(6HG)P*(6HT)P*(6HG)P*(6HG)P*(6HC)P*CP*GP*TP*GP*GP*TP*C)-3')
P: DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,38711
Polymers98,9213
Non-polymers4668
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8180 Å2
ΔGint-35 kcal/mol
Surface area37860 Å2
Unit cell
Length a, b, c (Å)69.081, 112.312, 77.971
Angle α, β, γ (deg.)90.000, 108.503, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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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 TP

#2: DNA chain DNA (5'-D(P*AP*CP*(6HT)P*(6HG)P*(6HT)P*(6HG)P*(6HG)P*(6HC)P*CP*GP*TP*GP*GP*TP*C)-3')


Mass: 5014.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: 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)

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Non-polymers , 3 types, 20 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG 4000, 20% v/v glycerol, 0.02 M d-glucose, 0.02 M d-mannose, 0.02 M d-galactose, 0.02 M l-fucose, 0.02 M d-xylose, 0.02 M N-acetyl-d-glucosamine, 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: SLS / Beamline: X06SA / Wavelength: 1.00002 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.31→44.72 Å / Num. obs: 95106 / % possible obs: 97 % / Redundancy: 1.82 % / CC1/2: 0.989 / Net I/σ(I): 3.48
Reflection shellResolution: 2.31→2.45 Å / Num. unique obs: 15434 / CC1/2: 0.104 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→44.72 Å / SU ML: 0.5672 / Cross valid method: FREE R-VALUE / σ(F): 1.03 / Phase error: 35.7854
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2855 2977 4.01 %
Rwork0.2255 71189 -
obs0.2278 74166 97.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.43 Å2
Refinement stepCycle: LAST / Resolution: 2.51→44.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6192 576 28 12 6808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00346985
X-RAY DIFFRACTIONf_angle_d0.65599513
X-RAY DIFFRACTIONf_chiral_restr0.04221022
X-RAY DIFFRACTIONf_plane_restr0.00491120
X-RAY DIFFRACTIONf_dihedral_angle_d21.1792706
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.550.52341400.43373371X-RAY DIFFRACTION95.9
2.55-2.590.51441450.43573416X-RAY DIFFRACTION97.45
2.59-2.640.45051380.4043383X-RAY DIFFRACTION98
2.64-2.690.38751410.36593425X-RAY DIFFRACTION98.16
2.69-2.740.34631440.35553443X-RAY DIFFRACTION98.01
2.74-2.80.37121400.34063370X-RAY DIFFRACTION97.91
2.8-2.870.34491460.32363502X-RAY DIFFRACTION98.17
2.87-2.940.29911390.31693339X-RAY DIFFRACTION97.7
2.94-3.020.41161500.31083412X-RAY DIFFRACTION97.96
3.02-3.110.34851450.3073390X-RAY DIFFRACTION97.25
3.11-3.210.37321410.30163421X-RAY DIFFRACTION97.48
3.21-3.320.3291390.28163340X-RAY DIFFRACTION96.26
3.33-3.460.36011400.24893364X-RAY DIFFRACTION96.13
3.46-3.620.26631400.23813283X-RAY DIFFRACTION94.87
3.62-3.810.2911380.21643398X-RAY DIFFRACTION97.12
3.81-4.040.26131430.20453405X-RAY DIFFRACTION97.88
4.04-4.360.24141390.17763427X-RAY DIFFRACTION97.91
4.36-4.790.23731410.15713380X-RAY DIFFRACTION97.37
4.79-5.490.2261480.16583392X-RAY DIFFRACTION97.17
5.49-6.910.28391390.18453343X-RAY DIFFRACTION96.06
6.91-44.720.17671410.13943385X-RAY DIFFRACTION97.22
Refinement TLS params.Method: refined / Origin x: 6.53378471558 Å / Origin y: -4.12925172501 Å / Origin z: 18.8941262898 Å
111213212223313233
T0.416175677395 Å2-0.017592213281 Å2-0.0260558554085 Å2-0.380812947691 Å2-0.0494464190138 Å2--0.467350378508 Å2
L0.709290642553 °20.0426161681346 °2-0.672883505132 °2-0.607102559194 °20.00764453064252 °2--1.17679408301 °2
S-0.0288040182819 Å °0.0991537614316 Å °-0.0522055939261 Å °-0.228954192526 Å °0.0709019936681 Å °-0.0551811452811 Å °0.0248805153038 Å °0.0796713925228 Å °-0.0400277955258 Å °
Refinement TLS groupSelection details: all

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