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- PDB-1hjp: HOLLIDAY JUNCTION BINDING PROTEIN RUVA FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 1hjp
TitleHOLLIDAY JUNCTION BINDING PROTEIN RUVA FROM E. COLI
ComponentsRUVARuvABC
KeywordsDNA RECOMBINATION / DNA REPAIR / HOLLIDAY JUNCTION BINDING
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 / Ubiquitin-associated (UBA) domain / RuvA domain 2-like / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 ...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 / Ubiquitin-associated (UBA) domain / RuvA domain 2-like / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Helicase, Ruva Protein; domain 3 / Nucleic acid-binding proteins / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Holliday junction branch migration complex subunit RuvA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.5 Å
AuthorsNishino, T. / Ariyoshi, M. / Iwasaki, H. / Shinagawa, H. / Morikawa, K.
CitationJournal: Structure / Year: 1998
Title: Functional Analyses of the Domain Structure in the Holliday Junction Binding Protein Ruva
Authors: Nishino, T. / Ariyoshi, M. / Iwasaki, H. / Shinagawa, H. / Morikawa, K.
History
DepositionAug 21, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 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: RUVA


Theoretical massNumber of molelcules
Total (without water)22,1121
Polymers22,1121
Non-polymers00
Water34219
1
A: RUVA

A: RUVA

A: RUVA

A: RUVA


Theoretical massNumber of molelcules
Total (without water)88,4474
Polymers88,4474
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area10480 Å2
ΔGint-52 kcal/mol
Surface area32630 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)83.730, 83.730, 34.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

#1: Protein RUVA / RuvABC


Mass: 22111.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: BL21 / Gene: RUVA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P0A809
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 45 %
Crystal growpH: 4.9
Details: 50MM CITRATE PH4.9 500MM NACL 10% GLYCEROL 3% PEG2000
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 4.8 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMcitrate11
21 mMdithiothreitol11
3500 mM11NaCl
410 %glycerol11
53-3.5 %PEG200011

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 29, 1996 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→80 Å / Num. obs: 7922 / % possible obs: 93.7 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 8.4
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 1.9 / % possible all: 80.5

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Processing

Software
NameClassification
X-PLORmodel building
REFMACrefinement
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.5→15 Å / Cross valid method: FREE R / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.294 769 10 %RANDOM
Rwork0.229 ---
obs-7916 93 %-
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1439 0 0 19 1458
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 7873 / Rfactor all: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS

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