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Open data
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Basic information
Entry | Database: PDB / ID: 1bi0 | ||||||
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Title | STRUCTURE OF APO-AND HOLO-DIPHTHERIA TOXIN REPRESSOR | ||||||
![]() | DIPHTHERIA TOXIN REPRESSOR | ||||||
![]() | REPRESSOR / TRANSCRIPTION REGULATION / DNA-BINDING / IRON | ||||||
Function / homology | ![]() transition metal ion binding / SH3 domain binding / protein dimerization activity / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Pohl, E. / Hol, W.G. | ||||||
![]() | ![]() Title: Motion of the DNA-binding domain with respect to the core of the diphtheria toxin repressor (DtxR) revealed in the crystal structures of apo- and holo-DtxR. Authors: Pohl, E. / Holmes, R.K. / Hol, W.G. #1: ![]() Title: Three-Dimensional Structure of the Diphtheria Toxin Repressor in Complex with Divalent Cation Co-Repressors Authors: Qiu, X. / Verlinde, C.L. / Zhang, S. / Schmitt, M.P. / Holmes, R.K. / Hol, W.G. #2: ![]() Title: Purification and Characterization of the Diphtheria Toxin Repressor Authors: Schmitt, M.P. / Twiddy, E.M. / Holmes, R.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54.2 KB | Display | ![]() |
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PDB format | ![]() | 41.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 416.4 KB | Display | ![]() |
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Full document | ![]() | 420.7 KB | Display | |
Data in XML | ![]() | 7.1 KB | Display | |
Data in CIF | ![]() | 10.3 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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Unit cell |
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Components
#1: Protein | Mass: 25381.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 57 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop / Details: Qiu, X., (1995) Structure (London), 3, 87. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Aug 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→8 Å / Num. obs: 10884 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 10 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 10 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 9 / Rsym value: 0.237 / % possible all: 99.9 |
Reflection | *PLUS % possible obs: 96.2 % / Num. measured all: 102464 / Rmerge(I) obs: 0.083 |
Reflection shell | *PLUS % possible obs: 99.9 % |
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Processing
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Refinement | Method to determine structure: ![]() Details: 2FO-FC ELECTRON DENSITY IS MISSING FOR RESIDUES 1 - 3, 141 - 147 AND 199 - 200. THESE RESIDUES ARE ASSUMED TO BE DISORDERED. THE EXPERIMENTAL ELECTRON DENSITY IS WEAK OR MISSING FOR RESIDUES 148 - 226.
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Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Software | *PLUS Name: ![]() | ||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.191 / Rfactor Rwork: 0.19 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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