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- PDB-1pjr: STRUCTURE OF DNA HELICASE -

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Basic information

Entry
Database: PDB / ID: 1pjr
TitleSTRUCTURE OF DNA HELICASE
ComponentsPCRA
KeywordsHELICASE / DNA REPAIR / DNA REPLICATION / SOS RESPONSE / ATP-BINDING / DNA-BINDING
Function / homology
Function and homology information


DNA helicase complex / recombinational repair / DNA 3'-5' helicase / 3'-5' DNA helicase activity / DNA unwinding involved in DNA replication / isomerase activity / ATP hydrolysis activity / DNA binding / ATP binding / cytosol
Similarity search - Function
ATP-dependent DNA helicase PcrA / PcrA/UvrD tudor domain / Arc Repressor Mutant, subunit A - #160 / PCRA; domain 4 / PCRA; domain 4 / DExx box DNA helicase domain superfamily / UvrD-like DNA helicase C-terminal domain profile. / UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain ...ATP-dependent DNA helicase PcrA / PcrA/UvrD tudor domain / Arc Repressor Mutant, subunit A - #160 / PCRA; domain 4 / PCRA; domain 4 / DExx box DNA helicase domain superfamily / UvrD-like DNA helicase C-terminal domain profile. / UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type / UvrD-like helicase, ATP-binding domain / Arc Repressor Mutant, subunit A / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ATP-dependent DNA helicase PcrA
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsSubramanya, H.S. / Bird, L.E. / Brannigan, J.A. / Wigley, D.B.
CitationJournal: Nature / Year: 1996
Title: Crystal structure of a DExx box DNA helicase.
Authors: Subramanya, H.S. / Bird, L.E. / Brannigan, J.A. / Wigley, D.B.
History
DepositionOct 11, 1996Processing site: BNL
Revision 1.0Dec 3, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PCRA


Theoretical massNumber of molelcules
Total (without water)82,5951
Polymers82,5951
Non-polymers00
Water4,053225
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.060, 139.060, 111.740
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein PCRA


Mass: 82595.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Strain: NCA1503 / Gene: PCRA / Plasmid: PET22 / Gene (production host): PCRA / Production host: Escherichia coli (E. coli) / References: UniProt: P56255
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.77 Å3/Da / Density % sol: 67 %
Crystal grow
*PLUS
pH: 6.4 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.2 Msodium acetate11
2100 mMMES11

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Data collection

Diffraction sourceWavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Aug 8, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionNum. obs: 40415 / % possible obs: 96.6 % / Redundancy: 2.36 % / Rmerge(I) obs: 0.049
Reflection
*PLUS
Highest resolution: 2.5 Å
Reflection shell
*PLUS
% possible obs: 98.8 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 2.5→10 Å
RfactorNum. reflection
Rfree0.269 -
Rwork0.215 -
obs0.215 38420
Displacement parametersBiso mean: 37.07 Å2
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5053 0 0 225 5278
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg2.94
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 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 2.96

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