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Open data
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Basic information
Entry | Database: PDB / ID: 2vub | ||||||
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Title | CCDB, A TOPOISOMERASE POISON FROM E. COLI | ||||||
![]() | CCDB | ||||||
![]() | CCDB / TOPOISOMERASE POISON / PLASMID | ||||||
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 | ![]() | 166.3 KB | Display | ![]() |
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PDB format | ![]() | 135.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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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.: 8 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: 2.74 Å3/Da / Density % sol: 55.03 % | ||||||||||||||||
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Crystal grow | pH: 9 / Details: pH 9.0 | ||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 9 / PH range high: 6.5 | ||||||||||||||||
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: 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: 2.45→15 Å / Num. obs: 36967 / % possible obs: 96.3 % / Redundancy: 4.86 % / Rsym value: 0.093 / Net I/σ(I): 14.39 |
Reflection shell | Resolution: 2.45→2.56 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 3.76 / Rsym value: 0.422 / % possible all: 92.2 |
Reflection | *PLUS Num. measured all: 179543 / Rmerge(I) obs: 0.093 |
Reflection shell | *PLUS % possible obs: 92.2 % / Rmerge(I) obs: 0.422 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: TETRAGONAL CRYSTAL FORM OF CCDB Resolution: 2.45→15 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
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Refinement step | Cycle: LAST / Resolution: 2.45→15 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.45→2.56 Å / Total num. of bins used: 8
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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