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Open data
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Basic information
Entry | Database: PDB / ID: 1vub | ||||||
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Title | CCDB, A TOPOISOMERASE POISON FROM E. COLI | ||||||
![]() | CCDB | ||||||
![]() | PLASMID / CCDB / TOPOISOMERASE POISON / PLASMID ADDICTION | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Loris, R. / Dao-Thi, M.-H. / Bahasi, E.M. / Van Melderen, L. / Poortmans, F. / Liddington, R. / Couturier, M. / Wyns, L. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.4 KB | Display | ![]() |
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PDB format | ![]() | 69.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 378.8 KB | Display | ![]() |
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Full document | ![]() | 383.9 KB | Display | |
Data in XML | ![]() | 8.3 KB | Display | |
Data in CIF | ![]() | 13.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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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.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.26 |