+Open data
-Basic information
Entry | Database: PDB / ID: 2cvh | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the RadB recombinase | ||||||
Components | DNA repair and recombination protein radB | ||||||
Keywords | DNA 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 | ||||||
Biological species | Thermococcus kodakarensis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Akiba, T. / Ishii, N. / Rashid, N. / Morikawa, M. / Imanaka, T. / Harata, K. | ||||||
Citation | Journal: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2cvh.cif.gz | 102.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2cvh.ent.gz | 79.5 KB | Display | PDB format |
PDBx/mmJSON format | 2cvh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cvh_validation.pdf.gz | 437.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2cvh_full_validation.pdf.gz | 460.6 KB | Display | |
Data in XML | 2cvh_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 2cvh_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/2cvh ftp://data.pdbj.org/pub/pdb/validation_reports/cv/2cvh | HTTPS FTP |
-Related structure data
Related structure data | 2cvfSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | 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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49.2 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 20% PEG 6000, 2.0M lithium sulphate, 50mM citrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å |
Detector | Type: ADSC QUAMTUM 4r / Detector: CCD / Date: Feb 1, 2003 / Details: mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→29.88 Å / Num. obs: 31513 / % possible obs: 99.8 % / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.03→2.14 Å / % possible all: 99.6 |
-Processing
Software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CVF Resolution: 2.2→6 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→6 Å
|