+Open data
-Basic information
Entry | Database: PDB / ID: 4vub | ||||||
---|---|---|---|---|---|---|---|
Title | CCDB, A TOPOISOMERASE POISON FROM ESCHERICHIA COLI | ||||||
Components | CCDBChristian Commission for Development in Bangladesh | ||||||
Keywords | PLASMID / CCDB / TOPOISOMERASE POISON / PLASMID ADDICTION | ||||||
Function / homology | Function and homology information DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity / negative regulation of DNA-templated DNA replication / toxin-antitoxin complex / plasmid maintenance / transcription repressor complex / negative regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR SUBSTITUTION / Resolution: 1.45 Å | ||||||
Authors | Loris, R. / Dao-Thi, M.-H. / Bahasi, E.M. / Van Melderen, L. / Poortmans, F. / Liddington, R. / Couturier, M. / Wyns, L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Crystal structure of CcdB, a topoisomerase poison from E. coli. Authors: Loris, R. / Dao-Thi, M.-H. / Bahassi, E.M. / Van Melderen, L. / Poortmans, F. / Liddington, R. / Couturier, M. / Wyns, L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4vub.cif.gz | 37.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4vub.ent.gz | 25.6 KB | Display | PDB format |
PDBx/mmJSON format | 4vub.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vu/4vub ftp://data.pdbj.org/pub/pdb/validation_reports/vu/4vub | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 11721.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MS501 / Gene: CCDB / Plasmid: PULB2250 / Gene (production host): CCDB / Production host: Escherichia coli (E. coli) / Strain (production host): MS501 / References: UniProt: P62554 | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 35.05 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 4.5 / Details: pH 4.5 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: Dao-Thi, M.H., (1997) Acta Crystallog. sect D., 54, 975. PH range low: 8.5 / PH range high: 7.5 | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 120 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR590 / Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jan 1, 1997 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→15 Å / Num. obs: 40715 / % possible obs: 83.7 % / Redundancy: 3.1 % / Rsym value: 0.087 / Net I/σ(I): 18.62 |
Reflection shell | Resolution: 1.45→1.55 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 5.36 / Rsym value: 0.189 / % possible all: 58.7 |
Reflection | *PLUS Rmerge(I) obs: 0.087 |
Reflection shell | *PLUS % possible obs: 58.7 % / Rmerge(I) obs: 0.189 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR SUBSTITUTION Starting model: REFINEMENT STARTED FROM REFINED COORDINATES OF THE SAME STRUCTURE AT ROOM TEMPERATURE Resolution: 1.45→15 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.45→1.52 Å / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|