+Open data
-Basic information
Entry | Database: PDB / ID: 1vub | ||||||
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Title | CCDB, A TOPOISOMERASE POISON FROM E. 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 REPLACEMENT / Resolution: 2.6 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vub.cif.gz | 89.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vub.ent.gz | 69.3 KB | Display | PDB format |
PDBx/mmJSON format | 1vub.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vu/1vub ftp://data.pdbj.org/pub/pdb/validation_reports/vu/1vub | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 11721.508 Da / Num. of mol.: 4 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 | ChemComp-CL / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.22 % | ||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||
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
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1993 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→10 Å / Num. obs: 101106 / % possible obs: 93 % / Redundancy: 6.82 % / Rsym value: 0.098 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2.89 / Rsym value: 0.333 / % possible all: 77.6 |
Reflection | *PLUS Num. obs: 14825 / Num. measured all: 101106 / Rmerge(I) obs: 0.098 |
Reflection shell | *PLUS % possible obs: 77.6 % / Rmerge(I) obs: 0.333 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PRELIMINARY MIR MODEL IN DIFFERENT CRYSTAL FORM Resolution: 2.6→10 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.6→10 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.72 Å / Total num. of bins used: 8
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.26 |