+Open data
-Basic information
Entry | Database: PDB / ID: 3jsc | ||||||
---|---|---|---|---|---|---|---|
Title | CcdBVfi-FormI-pH7.0 | ||||||
Components | CcdBChristian Commission for Development in Bangladesh | ||||||
Keywords | TOXIN / ALPHA+BETA / SH3 domain | ||||||
Function / homology | Function and homology information DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity / plasmid maintenance Similarity search - Function | ||||||
Biological species | Vibrio fischeri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | De Jonge, N. / Buts, L. / Loris, R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Structural and thermodynamic characterization of vibrio fischeri CCDB Authors: De Jonge, N. / Hohlweg, W. / Garcia-Pino, A. / Respondek, M. / Buts, L. / Haesaerts, S. / Lah, J. / Zangger, K. / Loris, R. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2007 Title: Purification and crystallization of Vibrio fischeri CcdB and its complexes with fragments of gyrase and CcdA Authors: De Jonge, N. / Buts, L. / Vangelooven, J. / Mine, N. / Van Melderen, L. / Wyns, L. / Loris, R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3jsc.cif.gz | 33.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3jsc.ent.gz | 22.7 KB | Display | PDB format |
PDBx/mmJSON format | 3jsc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/js/3jsc ftp://data.pdbj.org/pub/pdb/validation_reports/js/3jsc | HTTPS FTP |
---|
-Related structure data
Related structure data | 2kmtC 3jrzC 1vubS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 11879.721 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: tac promotor / Source: (gene. exp.) Vibrio fischeri (bacteria) / Gene: ccdB / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): B462 / References: UniProt: Q84B82 |
---|---|
#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.85 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 50mM Tris pH 7.0, 35% PEG 400, 250mM LiSO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8162 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 12, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8162 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→19.914 Å / Num. all: 16225 / Num. obs: 16225 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 18.89 % / Biso Wilson estimate: 14.55 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 34.2 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 18.9 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 12.1 / Num. unique all: 1589 / Rsym value: 0.176 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CcdB from monomer A (1VUB) Resolution: 1.5→19.914 Å / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.88 / SU ML: 0.17 / Isotropic thermal model: individual atomic B factors / Cross valid method: THROUGHOUT / σ(F): 1.35 / σ(I): 0 / Phase error: 18.65 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 94.461 Å2 / ksol: 0.454 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 48.82 Å2 / Biso mean: 17.692 Å2 / Biso min: 7.5 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→19.914 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|