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- PDB-1tgo: THERMOSTABLE B TYPE DNA POLYMERASE FROM THERMOCOCCUS GORGONARIUS -

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Basic information

Entry
Database: PDB / ID: 1tgo
TitleTHERMOSTABLE B TYPE DNA POLYMERASE FROM THERMOCOCCUS GORGONARIUS
ComponentsPROTEIN (THERMOSTABLE B DNA POLYMERASE)
KeywordsTRANSFERASE / DNA POLYMERASE / REPLICATION / DISULFIDE BONDS
Function / homology
Function and homology information


nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / base-excision repair, gap-filling / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding
Similarity search - Function
B family DNA polymerase, thumb domain / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / Topoisomerase I; Chain A, domain 4 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site ...B family DNA polymerase, thumb domain / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / Topoisomerase I; Chain A, domain 4 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / 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 gorgonarius (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.5 Å
AuthorsHopfner, K.-P. / Eichinger, A. / Engh, R.A. / Laue, F. / Ankenbauer, W. / Huber, R. / Angerer, B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius.
Authors: Hopfner, K.P. / Eichinger, A. / Engh, R.A. / Laue, F. / Ankenbauer, W. / Huber, R. / Angerer, B.
History
DepositionFeb 23, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 22, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (THERMOSTABLE B DNA POLYMERASE)


Theoretical massNumber of molelcules
Total (without water)89,9521
Polymers89,9521
Non-polymers00
Water6,107339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.110, 105.220, 154.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein PROTEIN (THERMOSTABLE B DNA POLYMERASE) / EC 2.7.7.7


Mass: 89952.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus gorgonarius (archaea) / Cellular location: CYTOPLASM / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P56689, DNA-directed DNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O

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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: 2.62 Å3/Da / Density % sol: 53.03 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.2 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mg/mlprotein1drop
220 mMsodium phosphate1drop
310 mM2-mercaptoethanol1drop
4500 mM1dropNaCl
5100 mMTris1reservoir
62.0 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 30451 / % possible obs: 0.91 % / Redundancy: 7.9 % / Rsym value: 0.071
Reflection
*PLUS
Num. measured all: 482448 / Rmerge(I) obs: 0.071
Reflection shell
*PLUS
% possible obs: 86 % / Rmerge(I) obs: 0.262

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CCP4model building
CNS0.3refinement
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.5→25 Å / Data cutoff high rms absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE 7 C-TERMINAL RESIDUES WERE MODELED BY A POLY-ALANINE CHAIN INTO WEAK ELECTRON DENSITY TER ALA: THE SIX C-TERMINAL RESIDUES WERE WEAKLY SEEN IN THE ELECTRON DENSITY MAP AND MODELED BY POLY-ALANINE
RfactorNum. reflection% reflectionSelection details
Rfree0.271 -5 %RANDOM
Rwork0.209 ---
all-30451 --
obs-30451 91 %-
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6328 0 0 339 6667
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.417
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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