+Open data
-Basic information
Entry | Database: PDB / ID: 1bi0 | ||||||
---|---|---|---|---|---|---|---|
Title | STRUCTURE OF APO-AND HOLO-DIPHTHERIA TOXIN REPRESSOR | ||||||
Components | DIPHTHERIA TOXIN REPRESSOR | ||||||
Keywords | REPRESSOR / TRANSCRIPTION REGULATION / DNA-BINDING / IRON | ||||||
Function / homology | Function and homology information 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 | Corynebacterium diphtheriae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Pohl, E. / Hol, W.G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1998 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: Journal: Structure / Year: 1995 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: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992 Title: Purification and Characterization of the Diphtheria Toxin Repressor Authors: Schmitt, M.P. / Twiddy, E.M. / Holmes, R.K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1bi0.cif.gz | 54.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1bi0.ent.gz | 41.5 KB | Display | PDB format |
PDBx/mmJSON format | 1bi0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bi0_validation.pdf.gz | 416.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1bi0_full_validation.pdf.gz | 420.7 KB | Display | |
Data in XML | 1bi0_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 1bi0_validation.cif.gz | 10.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/1bi0 ftp://data.pdbj.org/pub/pdb/validation_reports/bi/1bi0 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 25381.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Strain: C7(-) / Gene: DTXR / Plasmid: PMS298 / Gene (production host): T / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-ALPHA / References: UniProt: P33120, UniProt: P0DJL7*PLUS |
---|---|
#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 57 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
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 % |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→8 Å / Cross valid method: R-FREE / σ(F): 2 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.
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
| ||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.191 / Rfactor Rwork: 0.19 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
|