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- PDB-8s87: KOD-H4 DNA polymerase mutant - apo structure -

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Basic information

Entry
Database: PDB / ID: 8s87
TitleKOD-H4 DNA polymerase mutant - apo structure
ComponentsDNA polymerase
KeywordsTRANSFERASE / apo / mutant DNA polymerase / XNA / 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 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
Biological speciesThermococcus kodakarensis KOD1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,81418
Polymers89,9771
Non-polymers83717
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-152 kcal/mol
Surface area36130 Å2
Unit cell
Length a, b, c (Å)74.424, 110.629, 111.363
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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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Non-polymers , 5 types, 170 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 15% (w/v) PEG 3K, 20% (v/v) 1,2,4-butantriol, 1% (w/v) NDSB 256, 0.03 M lithium sulfate, 0.03 M sodium sulfate, 0.03 M potassium sulfate, 0.1 M GlyGly/AMPD pH 8.5

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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: Apr 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.8→44.58 Å / Num. obs: 165421 / % possible obs: 99.9 % / Redundancy: 4.7 % / CC1/2: 0.992 / Net I/σ(I): 3.84
Reflection shellResolution: 1.8→1.91 Å / Num. unique obs: 26725 / CC1/2: 0.108 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(dev_4788: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→44.4 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.3 / Phase error: 43.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2708 3719 2.35 %
Rwork0.2299 --
obs0.2309 158305 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.82→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6178 0 42 153 6373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0166380
X-RAY DIFFRACTIONf_angle_d1.1288608
X-RAY DIFFRACTIONf_dihedral_angle_d5.656860
X-RAY DIFFRACTIONf_chiral_restr0.069921
X-RAY DIFFRACTIONf_plane_restr0.0121100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.840.59251330.60065533X-RAY DIFFRACTION96
1.84-1.870.60821340.615446X-RAY DIFFRACTION94
1.87-1.890.52421400.5735687X-RAY DIFFRACTION99
1.89-1.920.48891410.52565720X-RAY DIFFRACTION100
1.92-1.950.53681430.51165780X-RAY DIFFRACTION100
1.95-1.980.48741270.47725763X-RAY DIFFRACTION100
1.98-2.010.46981410.45635761X-RAY DIFFRACTION100
2.01-2.050.47911430.42915696X-RAY DIFFRACTION100
2.05-2.080.46381320.41455756X-RAY DIFFRACTION100
2.08-2.120.39541430.39285752X-RAY DIFFRACTION100
2.12-2.170.4461320.37975710X-RAY DIFFRACTION100
2.17-2.210.4371330.35155761X-RAY DIFFRACTION100
2.21-2.270.39311410.3065780X-RAY DIFFRACTION100
2.27-2.320.33741380.28795749X-RAY DIFFRACTION100
2.32-2.380.26861330.27735740X-RAY DIFFRACTION100
2.38-2.450.30771440.26655732X-RAY DIFFRACTION100
2.45-2.530.35031380.25615744X-RAY DIFFRACTION100
2.53-2.620.32881270.25215782X-RAY DIFFRACTION100
2.62-2.730.30321390.24345739X-RAY DIFFRACTION100
2.73-2.850.29311410.25495789X-RAY DIFFRACTION100
2.85-30.35461410.23175690X-RAY DIFFRACTION100
3-3.190.26721310.23675735X-RAY DIFFRACTION100
3.19-3.440.29911450.21715762X-RAY DIFFRACTION100
3.44-3.780.2341380.19025752X-RAY DIFFRACTION100
3.79-4.330.18511460.1595770X-RAY DIFFRACTION100
4.33-5.460.16221380.14275739X-RAY DIFFRACTION100
5.46-44.40.20251370.16415718X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -14.6368 Å / Origin y: 25.0941 Å / Origin z: -5.4945 Å
111213212223313233
T0.5725 Å2-0.0024 Å2-0.0422 Å2-0.4098 Å20.0212 Å2--0.3278 Å2
L0.1592 °2-0.0678 °2-0.091 °2-0.7406 °20.2346 °2--0.5697 °2
S0.0199 Å °-0.0011 Å °0.038 Å °0.0625 Å °-0.078 Å °0.0177 Å °-0.05 Å °-0.0081 Å °0.0552 Å °
Refinement TLS groupSelection details: all

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