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- PDB-1bdx: E. COLI DNA HELICASE RUVA WITH BOUND DNA HOLLIDAY JUNCTION, ALPHA... -

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Basic information

Entry
Database: PDB / ID: 1bdx
TitleE. COLI DNA HELICASE RUVA WITH BOUND DNA HOLLIDAY JUNCTION, ALPHA CARBONS AND PHOSPHATE ATOMS ONLY
Components
  • DNA (5'-D(P*GP*CP*AP*TP*GP*CP*AP*TP*AP*TP*GP*CP*AP*TP*GP*C)-3')
  • HOLLIDAY JUNCTION DNA HELICASE RUVA
KeywordsTRANSFERASE/DNA / DNA-BINDING / BRANCH MIGRATION / HOLLIDAY JUNCTION / RUV / COMPLEX DNA-BINDING PROTEIN-DNA / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


Holliday junction helicase complex / Holliday junction resolvase complex / four-way junction helicase activity / recombinational repair / SOS response / four-way junction DNA binding / response to radiation / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Holliday junction DNA helicase RuvA, C-terminal / DNA helicase, Holliday junction RuvA type, domain I, bacterial / RuvA, C-terminal domain superfamily / RuvA N terminal domain / RuvA, C-terminal domain / Bacterial DNA recombination protein RuvA / RuvA domain 2-like / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / Holliday junction branch migration complex subunit RuvA
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, MIR / Resolution: 6 Å
AuthorsHargreaves, D. / Rice, D.W. / Sedelnikova, S.E. / Artymiuk, P.J. / Lloyd, R.G. / Rafferty, J.B.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: Crystal structure of E.coli RuvA with bound DNA Holliday junction at 6 A resolution.
Authors: Hargreaves, D. / Rice, D.W. / Sedelnikova, S.E. / Artymiuk, P.J. / Lloyd, R.G. / Rafferty, J.B.
#1: Journal: Science / Year: 1996
Title: Crystal Structure of DNA Recombination Protein Ruva and a Model for its Binding to the Holliday Junction
Authors: Rafferty, J.B. / Sedelnikova, S.E. / Hargreaves, D. / Artymiuk, P.J. / Baker, P.J. / Sharples, G.J. / Mahdi, A.A. / Lloyd, R.G. / Rice, D.W.
History
DepositionMay 11, 1998Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
J: DNA (5'-D(P*GP*CP*AP*TP*GP*CP*AP*TP*AP*TP*GP*CP*AP*TP*GP*C)-3')
K: DNA (5'-D(P*GP*CP*AP*TP*GP*CP*AP*TP*AP*TP*GP*CP*AP*TP*GP*C)-3')
L: DNA (5'-D(P*GP*CP*AP*TP*GP*CP*AP*TP*AP*TP*GP*CP*AP*TP*GP*C)-3')
M: DNA (5'-D(P*GP*CP*AP*TP*GP*CP*AP*TP*AP*TP*GP*CP*AP*TP*GP*C)-3')
A: HOLLIDAY JUNCTION DNA HELICASE RUVA
B: HOLLIDAY JUNCTION DNA HELICASE RUVA
C: HOLLIDAY JUNCTION DNA HELICASE RUVA
D: HOLLIDAY JUNCTION DNA HELICASE RUVA


Theoretical massNumber of molelcules
Total (without water)108,0398
Polymers108,0398
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.000, 148.000, 105.600
Angle α, β, γ (deg.)90.00, 123.00, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99999, 0.00034, 0.00518), (0.00034, -0.99149, 0.13018), (0.00518, 0.13018, 0.99148)73.71131, -3.18269, 0.01618
2given(1.0E-5, -0.9977, 0.06782), (0.99804, 0.00425, 0.06249), (-0.06264, 0.06769, 0.99574)35.26724, -38.3683, 2.41632
3given(1.0E-5, 0.99804, -0.06264), (-0.9977, 0.00426, 0.06769), (0.06782, 0.0625, 0.99574)38.44391, 35.18567, -2.40027

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Components

#1: DNA chain
DNA (5'-D(P*GP*CP*AP*TP*GP*CP*AP*TP*AP*TP*GP*CP*AP*TP*GP*C)-3') / Coordinate model: P atoms only


Mass: 4898.191 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein
HOLLIDAY JUNCTION DNA HELICASE RUVA / Coordinate model: Cα atoms only


Mass: 22111.668 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Species: Escherichia coli / Strain: BL21List of strains of Escherichia coli / Variant: DE3 / Plasmid: PAM159 / Species (production host): Escherichia coli / Gene (production host): RUVA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P0A809

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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: 4.46 Å3/Da / Density % sol: 48 %
Description: MOLECULAR REPLACEMENT PHASES WERE ONLY GOOD ENOUGH TO USE IN LOCATING HEAVY ATOMS BY DIFFERENCE FOURIER AND WERE THEN ABANDONED IN FAVOUR OF MIR PHASES.
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: PROTEIN/DNA COMPLEX WAS CRYSTALLISED FROM 0.85M SODIUM ACETATE BUFFERED WITH 100MM IMIDAZOLE AT PH 6.5, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM ACETATE11
2IMIDAZOLE11
3SODIUM ACETATE12
4IMIDAZOLE12
Crystal grow
*PLUS
Details: Hargreaves, D., (1999) Acta. Crystallogr., D55, 263.
PH range low: 7.5 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19 mg/mlprotein1drop
20.1 Mimidazole-HCl1reservoir
30.70-0.95 Msodium acetate1reservoir
41

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1997 / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 5.7→17.6 Å / Num. obs: 5263 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 6.8
Reflection shellResolution: 5.7→6.01 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.224 / % possible all: 94.2
Reflection
*PLUS
% possible obs: 94 % / Num. measured all: 10906

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Processing

Software
NameVersionClassification
CCP4model building
MLPHAREphasing
Omodel building
DENZOdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
CCP4phasing
TFFCphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, MIR
Starting model: 1CUK

1cuk


Highest resolution: 6 Å
Details: OWING TO THE LOW RESOLUTION OF THE DATA, NO POSITIONAL REFINEMENT OF THE PROTEIN RESIDUES OR DNA WAS PERFORMED
Refinement stepCycle: LAST / Highest resolution: 6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms760 64 0 0 824

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