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- PDB-1hqc: STRUCTURE OF RUVB FROM THERMUS THERMOPHILUS HB8 -

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Basic information

Entry
Database: PDB / ID: 1hqc
TitleSTRUCTURE OF RUVB FROM THERMUS THERMOPHILUS HB8
ComponentsRUVBRuvABC
KeywordsHYDROLASE / extended AAA-ATPase domain / RuvB / complex with nucleotide
Function / homology
Function and homology information


Holliday junction resolvase complex / four-way junction helicase activity / four-way junction DNA binding / DNA helicase / DNA recombination / DNA repair / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
DNA helicase, Holliday junction RuvB-type / RuvB C-terminal winged helix domain / RuvB, AAA lid domain / RuvB C-terminal winged helix domain / RuvB AAA lid domain / RuvB-like P-loop domain / Holliday junction DNA helicase RuvB P-loop domain / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...DNA helicase, Holliday junction RuvB-type / RuvB C-terminal winged helix domain / RuvB, AAA lid domain / RuvB C-terminal winged helix domain / RuvB AAA lid domain / RuvB-like P-loop domain / Holliday junction DNA helicase RuvB P-loop domain / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENINE / Holliday junction branch migration complex subunit RuvB
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.2 Å
AuthorsYamada, K. / Kunishima, N. / Mayanagi, K. / Iwasaki, H. / Morikawa, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Crystal structure of the Holliday junction migration motor protein RuvB from Thermus thermophilus HB8.
Authors: Yamada, K. / Kunishima, N. / Mayanagi, K. / Ohnishi, T. / Nishino, T. / Iwasaki, H. / Shinagawa, H. / Morikawa, K.
History
DepositionDec 15, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RUVB
B: RUVB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4206
Polymers72,1012
Non-polymers3194
Water0
1
A: RUVB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2103
Polymers36,0511
Non-polymers1592
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RUVB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2103
Polymers36,0511
Non-polymers1592
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.865, 84.865, 355.24
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein RUVB / RuvABC


Mass: 36050.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: RUVB / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SL87, EC: 3.6.1.3
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADE / ADENINE / Adenine


Mass: 135.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5

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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: 4.43 Å3/Da / Density % sol: 72.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, sodium chloride, magnesium chloride, ADP, AMPPNP, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMTris-HCl1drop
20.35 M1dropNaCl
310 %glycerol1drop
41 %PEG40001drop
520 mMTris-HCl1reservoir
62.0 M1reservoirNaCl
710 %glycerol1reservoir
810 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.885 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 28, 1998
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885 Å / Relative weight: 1
ReflectionResolution: 3.2→12 Å / Num. all: 22248 / Num. obs: 21630 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 8.36

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 3.2→12 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2965 1062 RANDOM
Rwork0.2627 --
all-21997 -
obs-21241 -
Displacement parametersBiso mean: 102 Å2
Refinement stepCycle: LAST / Resolution: 3.2→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4922 0 22 0 4944
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.53
X-RAY DIFFRACTIONc_bond_d0.0084
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 12 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.263
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 102 Å2

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