+Open data
-Basic information
Entry | Database: PDB / ID: 2dtr | |||||||||
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Title | STRUCTURE OF 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 / Resolution: 1.9 Å | |||||||||
Authors | Qiu, X. / Pohl, E. / Hol, W.G. | |||||||||
Citation | Journal: Biochemistry / Year: 1996 Title: High-resolution structure of the diphtheria toxin repressor complexed with cobalt and manganese reveals an SH3-like third domain and suggests a possible role of phosphate as co-corepressor. Authors: Qiu, X. / Pohl, E. / Holmes, R.K. / Hol, W.G. #1: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dtr.cif.gz | 49.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dtr.ent.gz | 31.4 KB | Display | PDB format |
PDBx/mmJSON format | 2dtr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dtr_validation.pdf.gz | 379.3 KB | Display | wwPDB validaton report |
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Full document | 2dtr_full_validation.pdf.gz | 379.7 KB | Display | |
Data in XML | 2dtr_validation.xml.gz | 4.3 KB | Display | |
Data in CIF | 2dtr_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/2dtr ftp://data.pdbj.org/pub/pdb/validation_reports/dt/2dtr | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25349.795 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Strain: C7(-) / Gene: T / Plasmid: PMS298 / Gene (production host): T / Production host: Escherichia coli (E. coli) / References: UniProt: P33120, UniProt: P0DJL7*PLUS |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-CO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 57 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 14788 / % possible obs: 78 % / Redundancy: 3 % / Rmerge(I) obs: 0.045 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 50 Å / Num. measured all: 41868 / Rmerge(I) obs: 0.045 |
Reflection shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.25 Å / % possible obs: 52 % |
-Processing
Software |
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Refinement | Resolution: 1.9→7 Å / σ(F): 1 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: 1.9→7 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.0171 / Lowest resolution: 7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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