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- PDB-2cvf: Crystal structure of the RadB recombinase -

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Basic information

Entry
Database: PDB / ID: 2cvf
TitleCrystal structure of the RadB recombinase
ComponentsDNA repair and recombination protein radB
KeywordsDNA BINDING PROTEIN / RadB / filament formation / homologous recombination / ATPase domain / hyperthermophile
Function / homology
Function and homology information


ATP-dependent DNA damage sensor activity / DNA recombination / damaged DNA binding / DNA repair / ATP binding
Similarity search - Function
DNA repair and recombination protein RadB / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA repair and recombination protein RadB
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.6 Å
AuthorsAkiba, T. / Ishii, N. / Rashid, N. / Morikawa, M. / Imanaka, T. / Harata, K.
CitationJournal: Nucleic Acids Res. / Year: 2005
Title: Structure of RadB recombinase from a hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1: an implication for the formation of a near-7-fold helical assembly
Authors: Akiba, T. / Ishii, N. / Rashid, N. / Morikawa, M. / Imanaka, T. / Harata, K.
History
DepositionJun 3, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 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: DNA repair and recombination protein radB
B: DNA repair and recombination protein radB


Theoretical massNumber of molelcules
Total (without water)49,1572
Polymers49,1572
Non-polymers00
Water4,702261
1
A: DNA repair and recombination protein radB


Theoretical massNumber of molelcules
Total (without water)24,5781
Polymers24,5781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA repair and recombination protein radB


Theoretical massNumber of molelcules
Total (without water)24,5781
Polymers24,5781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.014, 82.468, 111.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA repair and recombination protein radB


Mass: 24578.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: Pk-REC / Plasmid: pET-8c / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE)pLysS / References: UniProt: P95547
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.2 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M ammonium sulphate, 30% polyethylene glycol monomethyl ether 2000, 0.1M acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: May 11, 2002 / Details: Osmic Confocal Max-Flux optics
RadiationMonochromator: Osmic Confocal Max-Flux optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→24.7 Å / Num. obs: 16828 / % possible obs: 99.5 % / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.53 Å / % possible all: 98.7

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Processing

Software
NameVersionClassification
SMARTdata collection
SAINTdata reduction
SHARPphasing
X-PLOR3.1refinement
SMARTdata reduction
SAINTPLUSdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.6→6 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.304 1183 RANDOM
Rwork0.235 --
obs-11912 -
Refinement stepCycle: LAST / Resolution: 2.6→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3458 0 0 261 3719

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