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- PDB-1wns: Crystal structure of family B DNA polymerase from hyperthermophil... -

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Basic information

Entry
Database: PDB / ID: 1wns
TitleCrystal structure of family B DNA polymerase from hyperthermophilic archaeon pyrococcus kodakaraensis KOD1
ComponentsDNA POLYMERASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


intron homing / intein-mediated protein splicing / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / base-excision repair, gap-filling / DNA-templated DNA replication / endonuclease activity / DNA-directed DNA polymerase ...intron homing / intein-mediated protein splicing / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / base-excision repair, gap-filling / DNA-templated DNA replication / endonuclease activity / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding
Similarity search - Function
DNA polymerase II intein domain IV / DNA polymerase II intein Domain IV / LAGLIDADG-like domain / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / Homing endonuclease, LAGLIDADG ...DNA polymerase II intein domain IV / DNA polymerase II intein Domain IV / LAGLIDADG-like domain / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / Homing endonuclease, LAGLIDADG / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Homing endonuclease / Hint domain superfamily / DNA polymerase family B, thumb domain / DNA polymerase family B signature. / 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-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H-like superfamily/Ribonuclease H / Helix Hairpins / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHashimoto, H. / Inoue, T. / Kai, Y. / Fujiwara, S. / Takagi, M. / Nishioka, M. / Imanaka, T.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal Structure of DNA Polymerase from Hyperthermophilic Archaeon Pyrococcus Kodakaraensis Kod1
Authors: Hashimoto, H. / Nishioka, M. / Fujiwara, S. / Takagi, M. / Imanaka, T. / Inoue, T. / Kai, Y.
History
DepositionAug 9, 2004Deposition site: PDBJ / Processing site: PDBJ
SupersessionAug 17, 2004ID: 1GCX
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 16, 2017Group: Data collection / Source and taxonomy / Category: diffrn_detector / entity_src_gen / Item: _diffrn_detector.detector

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA POLYMERASE


Theoretical massNumber of molelcules
Total (without water)90,1631
Polymers90,1631
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.640, 111.380, 111.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA POLYMERASE


Mass: 90162.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Plasmid: PET-8C / Production host: Escherichia coli (E. coli) / References: UniProt: P77933, DNA-directed DNA polymerase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: MPD, pH 5.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Feb 26, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 20298 / % possible obs: 88.1 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 8.7
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.345 / % possible all: 83.7

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Processing

SoftwareName: CNS / Version: 1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→35.24 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 156351.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.313 1631 9.7 %RANDOM
Rwork0.231 ---
obs0.231 16749 89.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.34 Å2 / ksol: 0.275 e/Å3
Displacement parametersBiso mean: 55.7 Å2
Baniso -1Baniso -2Baniso -3
1-24.2 Å20 Å20 Å2
2--1.85 Å20 Å2
3----26.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.74 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 3→35.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5703 0 0 0 5703
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it2.272
X-RAY DIFFRACTIONc_scbond_it1.622
X-RAY DIFFRACTIONc_scangle_it2.612.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.419 252 9.7 %
Rwork0.333 2336 -
obs--84.7 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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