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Open data
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Basic information
Entry | Database: PDB / ID: 3jsc | ||||||
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Title | CcdBVfi-FormI-pH7.0 | ||||||
![]() | CcdB | ||||||
![]() | TOXIN / ALPHA+BETA / SH3 domain | ||||||
Function / homology | ![]() DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity / plasmid maintenance Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | De Jonge, N. / Buts, L. / Loris, R. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 33.7 KB | Display | ![]() |
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PDB format | ![]() | 22.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.1 KB | Display | ![]() |
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Full document | ![]() | 423.3 KB | Display | |
Data in XML | ![]() | 6.8 KB | Display | |
Data in CIF | ![]() | 8.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2kmtC ![]() 3jrzC ![]() 1vubS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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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.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.85 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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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
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Refinement step | Cycle: LAST / Resolution: 1.5→19.914 Å
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Refine LS restraints |
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LS refinement shell |
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