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

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Basic information

Entry
Database: PDB / ID: 9emf
TitleKOD-H4 DNA polymerase mutant in a binary complex with DNA:DNA containing one HNA nucleotide
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*GP*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-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
Chem-6BX / 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 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(P*AP*CP*(6HT)P*GP*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,40512
Polymers98,8513
Non-polymers5549
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-92 kcal/mol
Surface area36740 Å2
Unit cell
Length a, b, c (Å)111.091, 148.602, 66.639
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(P*AP*CP*(6HT)P*GP*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')


Mass: 4944.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 18 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-6BX / (2S)-2-hydroxy-3-(morpholin-4-yl)propane-1-sulfonic acid


Mass: 225.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO5S
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.78 Å3/Da / Density % sol: 55.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 12.5 % (w/v) PEG 4K, 20 % (v/v) 1,2,6-hexanetriol, 0.02 M DL-arginine-HCl- 0.02 M DL-threonine, 0.02 M D-sorbitol, 0.02 DL-histidine-HCl*H2O, 0.02 M DL-5-hydroxylysine-HCl, 0.02 M trans-4- ...Details: 12.5 % (w/v) PEG 4K, 20 % (v/v) 1,2,6-hexanetriol, 0.02 M DL-arginine-HCl- 0.02 M DL-threonine, 0.02 M D-sorbitol, 0.02 DL-histidine-HCl*H2O, 0.02 M DL-5-hydroxylysine-HCl, 0.02 M trans-4-hydroxy-L-proline, 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: 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: 2.7→49.534 Å / Num. obs: 58227 / % possible obs: 99.9 % / Redundancy: 4.35 % / CC1/2: 0.991 / Net I/σ(I): 3.66
Reflection shellResolution: 2.7→2.87 Å / Num. unique obs: 9378 / CC1/2: 0.106 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→45.3 Å / SU ML: 0.5077 / Cross valid method: FREE R-VALUE / σ(F): 1.28 / Phase error: 34.1772
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.27 2709 6.4 %
Rwork0.2337 39625 -
obs0.236 42334 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 93.03 Å2
Refinement stepCycle: LAST / Resolution: 3→45.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6200 571 32 9 6812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00296998
X-RAY DIFFRACTIONf_angle_d0.54489550
X-RAY DIFFRACTIONf_chiral_restr0.041028
X-RAY DIFFRACTIONf_plane_restr0.00451123
X-RAY DIFFRACTIONf_dihedral_angle_d18.22552747
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.060.48251430.42462044X-RAY DIFFRACTION99.32
3.06-3.120.481380.41362087X-RAY DIFFRACTION99.64
3.12-3.180.41691450.39882121X-RAY DIFFRACTION99.74
3.18-3.250.40921400.36552050X-RAY DIFFRACTION99.55
3.25-3.330.37781480.34942101X-RAY DIFFRACTION99.65
3.33-3.410.40361390.33152096X-RAY DIFFRACTION99.38
3.41-3.50.31241430.30162082X-RAY DIFFRACTION99.78
3.5-3.60.31151490.28942051X-RAY DIFFRACTION99.77
3.6-3.720.3511470.26452093X-RAY DIFFRACTION99.64
3.72-3.850.3041430.25642078X-RAY DIFFRACTION99.91
3.85-4.010.27631410.23692102X-RAY DIFFRACTION99.56
4.01-4.190.23831450.23692102X-RAY DIFFRACTION99.91
4.19-4.410.29891400.20352073X-RAY DIFFRACTION99.64
4.41-4.690.21881430.18832094X-RAY DIFFRACTION99.96
4.69-5.050.22721450.19272076X-RAY DIFFRACTION99.73
5.05-5.550.23481370.20412115X-RAY DIFFRACTION99.87
5.56-6.360.26911420.20822082X-RAY DIFFRACTION100
6.36-80.20671390.19312085X-RAY DIFFRACTION99.87
8-45.30.17921420.15862093X-RAY DIFFRACTION99.47
Refinement TLS params.Method: refined / Origin x: 28.1254111721 Å / Origin y: 20.4248820992 Å / Origin z: 18.349606588 Å
111213212223313233
T0.558727641931 Å2-0.0422886944233 Å20.0204223823466 Å2-0.599808159189 Å20.0214465841276 Å2--0.859328995303 Å2
L0.908344765976 °20.0997380862363 °2-0.0553587491707 °2-0.762484525189 °2-0.189886331656 °2--0.416145133193 °2
S-0.00215439717677 Å °-0.0133473207694 Å °-0.387354920484 Å °-0.00675008531761 Å °-0.150521996599 Å °-0.330122478909 Å °0.159189496207 Å °0.0593409066301 Å °0.155943996327 Å °
Refinement TLS groupSelection details: all

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