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- PDB-1qht: DNA POLYMERASE FROM THERMOCOCCUS SP. 9ON-7 ARCHAEON -

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Basic information

Entry
Database: PDB / ID: 1qht
TitleDNA POLYMERASE FROM THERMOCOCCUS SP. 9ON-7 ARCHAEON
ComponentsPROTEIN (DNA POLYMERASE)
KeywordsTRANSFERASE / DNA POLYMERASE / ARCHAEA / HYPERTHERMOSTABLE / FAMILY B POLYMERASE / POL ALPHA FAMILY POLYMERASE
Function / homology
Function and homology information


DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding
Similarity search - Function
DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / 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, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site ...DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / 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, 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-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Helix Hairpins / 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 sp. (archaea)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.1 Å
AuthorsPark, H.-W. / Rodriguez, A.C. / Beese, L.S.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of a pol alpha family DNA polymerase from the hyperthermophilic archaeon Thermococcus sp. 9 degrees N-7.
Authors: Rodriguez, A.C. / Park, H.W. / Mao, C. / Beese, L.S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization and Preliminary Diffraction Analysis of a Hyperthermostable DNA Polymerase from a Thermococcus Archaeon
Authors: Zhou, M. / Mao, C. / Rodriguez, A.C. / Kiefer, J.R. / Kucera, R.B. / Beese, L.S.
History
DepositionMay 26, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (DNA POLYMERASE)


Theoretical massNumber of molelcules
Total (without water)89,8271
Polymers89,8271
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.300, 98.700, 112.600
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 (DNA POLYMERASE)


Mass: 89826.570 Da / Num. of mol.: 1 / Mutation: D141A,E143A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus sp. (archaea) / Strain: 9oN-7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q56366, DNA-directed DNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
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: 2.9 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 291 K / pH: 9
Details: MICRODIALYSIS AT 291 K: 4-7% PEG 1500, 10 MM NICL2, 100 MM GLYCINE-NAOH, PH 9.0 OR 9.1; 25 MICROLITERS OF 3.9 MG/ML PROTEIN
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13.9 mg/mlprotein11
2100 mMglycine-NaOH12
310 mM12NiCl2
44-7 %PEG150012

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 58956 / % possible obs: 94.2 % / Redundancy: 11 % / Rsym value: 0.055
Reflection
*PLUS
Num. measured all: 652420 / Rmerge(I) obs: 0.055

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1refinement
RefinementMethod to determine structure: MIR / Resolution: 2.1→25 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.312 -5 %RANDOM
Rwork0.245 ---
obs0.245 55813 93.5 %-
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5803 0 0 109 5912
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_deg1.263
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: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.25 Å / Rfactor Rfree: 0.308 / Rfactor Rwork: 0.239
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.26

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