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- PDB-9emi: KOD-H4 DNA polymerase mutant in a ternary complex containing six ... -

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Basic information

Entry
Database: PDB / ID: 9emi
TitleKOD-H4 DNA polymerase mutant in a ternary complex containing six HNA nucleotides and a non-hydrolyzable triphosphate
Components
  • DNA (5'-D(*(6HA)P*(6HA)P*(6HC)P*(6HT)P*(6HG)P*(6HT)P*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*(XG4))-3')
  • DNA polymerase
KeywordsTRANSFERASE / Polymerase / XNA / modified nucleotides / Reverse transcriptase / HNA / non-hydrolyzable triphosphate
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
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: 2.27 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 8, 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(*(6HA)P*(6HA)P*(6HC)P*(6HT)P*(6HG)P*(6HT)P*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,6629
Polymers98,9213
Non-polymers7416
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8830 Å2
ΔGint-25 kcal/mol
Surface area35670 Å2
Unit cell
Length a, b, c (Å)111.454, 151.548, 70.406
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(*(6HA)P*(6HA)P*(6HC)P*(6HT)P*(6HG)P*(6HT)P*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')


Mass: 5014.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 38 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 58.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG 8000, 20% v/v ethylene glycol 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 bicine/Trizma base pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.26→46.809 Å / Num. obs: 101092 / % possible obs: 93.7 % / Redundancy: 7 % / CC1/2: 0.996 / Net I/σ(I): 7.44
Reflection shellResolution: 2.26→2.4 Å / Num. unique obs: 17452 / CC1/2: 0.237

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Processing

Software
NameVersionClassification
PHENIX(dev_4788: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→41.04 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.3 / Phase error: 36.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2654 3816 3.86 %
Rwork0.2345 --
obs0.2357 98883 92.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.27→41.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6200 625 14 32 6871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037055
X-RAY DIFFRACTIONf_angle_d0.6419627
X-RAY DIFFRACTIONf_dihedral_angle_d18.6951128
X-RAY DIFFRACTIONf_chiral_restr0.0441030
X-RAY DIFFRACTIONf_plane_restr0.0041128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.30.50911220.50652990X-RAY DIFFRACTION79
2.3-2.330.4681500.4593761X-RAY DIFFRACTION99
2.33-2.360.45161500.44473782X-RAY DIFFRACTION100
2.36-2.390.43521510.44043804X-RAY DIFFRACTION100
2.39-2.430.41151530.42413809X-RAY DIFFRACTION100
2.43-2.470.44621530.39163751X-RAY DIFFRACTION100
2.47-2.510.40421540.38443816X-RAY DIFFRACTION100
2.51-2.550.34051550.36183760X-RAY DIFFRACTION100
2.55-2.60.40511480.37293814X-RAY DIFFRACTION100
2.6-2.650.42891470.3563715X-RAY DIFFRACTION98
2.65-2.70.4083610.37061442X-RAY DIFFRACTION38
2.7-2.760.37281510.32433771X-RAY DIFFRACTION100
2.76-2.820.32651560.32653803X-RAY DIFFRACTION100
2.82-2.890.34841510.32243769X-RAY DIFFRACTION100
2.89-2.970.38771480.31773784X-RAY DIFFRACTION100
2.97-3.060.31751560.29443850X-RAY DIFFRACTION100
3.06-3.160.32531520.27653749X-RAY DIFFRACTION100
3.16-3.270.32781470.26533824X-RAY DIFFRACTION100
3.27-3.40.35251520.24363782X-RAY DIFFRACTION100
3.4-3.560.255900.24462104X-RAY DIFFRACTION55
3.56-3.740.2415980.22242454X-RAY DIFFRACTION65
3.75-3.980.22941100.20422795X-RAY DIFFRACTION73
3.98-4.290.20441530.17343787X-RAY DIFFRACTION100
4.29-4.720.22021520.15253787X-RAY DIFFRACTION100
4.72-5.40.1871530.16483774X-RAY DIFFRACTION100
5.4-6.80.23821500.1863783X-RAY DIFFRACTION100
6.8-41.040.13591530.15553807X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -27.8382 Å / Origin y: 21.2684 Å / Origin z: -16.8289 Å
111213212223313233
T0.3858 Å2-0.0421 Å2-0.0066 Å2-0.423 Å2-0.0343 Å2--0.4716 Å2
L1.3166 °2-0.0101 °2-0.0429 °2-1.1104 °2-0.5602 °2--0.744 °2
S0.0141 Å °-0.0926 Å °-0.2172 Å °0.0101 Å °-0.0539 Å °-0.0349 Å °0.1131 Å °-0.0401 Å °0.0365 Å °
Refinement TLS groupSelection details: all

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