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- PDB-1d8l: E. COLI HOLLIDAY JUNCTION BINDING PROTEIN RUVA NH2 REGION LACKING... -

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Basic information

Entry
Database: PDB / ID: 1d8l
TitleE. COLI HOLLIDAY JUNCTION BINDING PROTEIN RUVA NH2 REGION LACKING DOMAIN III
ComponentsPROTEIN (HOLLIDAY JUNCTION DNA HELICASE RUVA)
KeywordsGENE REGULATION / OB-FOLD / HELIX-HAIRPIN-HELIX MOTIF
Function / homology
Function and homology information


Holliday junction helicase complex / Holliday junction resolvase complex / four-way junction helicase activity / SOS response / recombinational repair / four-way junction DNA binding / response to radiation / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Bacterial DNA recombination protein RuvA / 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 / RuvA domain 2-like / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 ...Bacterial DNA recombination protein RuvA / 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 / 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 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 / Resolution: 2.5 Å
AuthorsNishino, T. / Iwasaki, H. / Kataoka, M. / Ariyoshi, M. / Fujita, T. / Shinagawa, H. / Morikawa, K.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Modulation of RuvB function by the mobile domain III of the Holliday junction recognition protein RuvA.
Authors: Nishino, T. / Iwasaki, H. / Kataoka, M. / Ariyoshi, M. / Fujita, T. / Shinagawa, H. / Morikawa, K.
History
DepositionOct 25, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 7, 2024Group: 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 (HOLLIDAY JUNCTION DNA HELICASE RUVA)
B: PROTEIN (HOLLIDAY JUNCTION DNA HELICASE RUVA)


Theoretical massNumber of molelcules
Total (without water)32,9992
Polymers32,9992
Non-polymers00
Water39622
1
A: PROTEIN (HOLLIDAY JUNCTION DNA HELICASE RUVA)
B: PROTEIN (HOLLIDAY JUNCTION DNA HELICASE RUVA)

A: PROTEIN (HOLLIDAY JUNCTION DNA HELICASE RUVA)
B: PROTEIN (HOLLIDAY JUNCTION DNA HELICASE RUVA)


Theoretical massNumber of molelcules
Total (without water)65,9974
Polymers65,9974
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)79.600, 115.600, 34.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PROTEIN (HOLLIDAY JUNCTION DNA HELICASE RUVA)


Mass: 16499.352 Da / Num. of mol.: 2 / Fragment: NH2 REGION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET11 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A809
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.42 Å3/Da / Density % sol: 49.28 %
Crystal growpH: 4.6 / Details: pH 4.60
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 4.6 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMcitrate-NaOH11
21 mMdithiothreitol11
310 %glycerol11

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418
DetectorType: MAC Science DIP-2020 / Detector: IMAGE PLATE / Date: Jan 22, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 10073 / % possible obs: 85.6 % / Observed criterion σ(I): 1 / Redundancy: 5 % / Biso Wilson estimate: 57 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 17.3
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 15 Å / Num. obs: 9523 / Observed criterion σ(I): 1 / Redundancy: 5 % / Num. measured all: 49960 / Biso Wilson estimate: 57 Å2
Reflection shell
*PLUS
% possible obs: 79.3 % / Rmerge(I) obs: 0.309

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
RefinementResolution: 2.5→15 Å / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.32 471 RANDOM
Rwork0.243 --
obs0.247 9523 -
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2192 0 0 22 2214
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.243 / Rfactor Rfree: 0.32
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.006
X-RAY DIFFRACTIONp_angle_deg1.5

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