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- PDB-8s84: KOD-H4 DNA polymerase mutant in a ternary complex with DNA/DNA an... -

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Basic information

Entry
Database: PDB / ID: 8s84
TitleKOD-H4 DNA polymerase mutant in a ternary complex with DNA/DNA and non-hydrolyzable triphosphate
Components
  • DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*CP*A*(XG4))-3')
  • DNA (5'-D(P*AP*CP*TP*GP*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-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 polymerase family B signature. / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / 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 polymerase family B signature. / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / 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 / : / Chem-XG4 / DNA / DNA (> 10) / DNA polymerase
Similarity search - Component
Biological speciesThermococcus kodakarensis KOD1 (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsGutfreund, C. / Betz, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Structural insights into a DNA polymerase reading the xeno nucleic acid HNA.
Authors: Gutfreund, C. / Betz, K. / Abramov, M. / Coosemans, F. / Holliger, P. / Herdewijn, P. / Marx, A.
History
DepositionMar 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.year / _citation_author.identifier_ORCID

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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*(XG4))-3')
T: DNA (5'-D(P*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)99,77313
Polymers98,8373
Non-polymers93610
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.970, 152.462, 70.125
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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*(XG4))-3')


Mass: 3930.578 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*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 , 6 types, 24 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-XG4 / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#7: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.99 Å3/Da / Density % sol: 58.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Morpheus II condition A1: 36 % v/v of a 72% mix: 30% w/v PEG 3000, 40% v/v 1, 2, 4-Butanetriol, 2% w/v NDSB 256; 0.03 M Lithium sulfate, 0.03 M Sodium sulfate, 0.03 Potassium sulfate, 0.1 M MOPSO/Bis-Tris 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: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.35→46.796 Å / Num. obs: 95588 / % possible obs: 99.4 % / Redundancy: 3 % / CC1/2: 0.985 / Net I/σ(I): 3.75
Reflection shellResolution: 2.35→2.49 Å / Num. unique obs: 15411 / CC1/2: 0.1

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Processing

Software
NameVersionClassification
PHENIX(dev_4788: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→38.58 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.07 / Phase error: 40.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2755 3647 3.91 %
Rwork0.2368 --
obs0.2383 93177 96.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→38.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6200 601 23 14 6838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.628
X-RAY DIFFRACTIONf_dihedral_angle_d18.3981149
X-RAY DIFFRACTIONf_chiral_restr0.0431033
X-RAY DIFFRACTIONf_plane_restr0.0051129
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.380.5482950.49142438X-RAY DIFFRACTION69
2.38-2.410.53131190.47022877X-RAY DIFFRACTION81
2.41-2.440.46521280.47453213X-RAY DIFFRACTION91
2.44-2.480.44651360.46633433X-RAY DIFFRACTION95
2.48-2.520.46441360.50443459X-RAY DIFFRACTION98
2.52-2.560.48191430.42923494X-RAY DIFFRACTION99
2.56-2.610.41811480.41743546X-RAY DIFFRACTION100
2.61-2.650.43961430.37183528X-RAY DIFFRACTION100
2.65-2.70.38411480.35493600X-RAY DIFFRACTION99
2.7-2.760.38551430.35653506X-RAY DIFFRACTION100
2.76-2.820.341460.33813519X-RAY DIFFRACTION99
2.82-2.880.37531440.34973522X-RAY DIFFRACTION99
2.88-2.960.46441440.34473525X-RAY DIFFRACTION99
2.96-3.040.40651470.35043555X-RAY DIFFRACTION99
3.04-3.130.32741450.33773525X-RAY DIFFRACTION100
3.13-3.230.33021390.29873538X-RAY DIFFRACTION100
3.23-3.340.31571430.26993539X-RAY DIFFRACTION99
3.34-3.480.29471430.253534X-RAY DIFFRACTION100
3.48-3.630.25571470.23653524X-RAY DIFFRACTION100
3.63-3.820.28521450.22413535X-RAY DIFFRACTION99
3.83-4.060.23541480.19853523X-RAY DIFFRACTION99
4.06-4.380.24181440.16913522X-RAY DIFFRACTION98
4.38-4.820.17341420.16223510X-RAY DIFFRACTION100
4.82-5.510.23951430.17393527X-RAY DIFFRACTION100
5.51-6.940.27021450.19393566X-RAY DIFFRACTION99
6.94-38.580.16951430.15483472X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 27.8973 Å / Origin y: 21.1681 Å / Origin z: 18.1589 Å
111213212223313233
T0.4336 Å2-0.0253 Å2-0.0022 Å2-0.4491 Å2-0.0209 Å2--0.4001 Å2
L1.5542 °2-0.2812 °20.0145 °2-1.9699 °2-0.8823 °2--0.9673 °2
S-0.0392 Å °-0.0537 Å °-0.2014 Å °0.1405 Å °-0.0366 Å °-0.0068 Å °0.0335 Å °-0.0668 Å °0.0861 Å °
Refinement TLS groupSelection details: all

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