+Open data
-Basic information
Entry | Database: PDB / ID: 2tdx | |||||||||
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Title | DIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL | |||||||||
Components | DIPHTHERIA TOX REPRESSOR | |||||||||
Keywords | DNA BINDING PROTEIN / DNA-BINDING REGULATORY PROTEIN / DIPHTHERIA TOX REPRESSOR / TRANSCRIPTION REGULATION / DNA-BINDING PROTEIN / IRON-REGULATED REPRESSOR | |||||||||
Function / homology | Function and homology information transition metal ion binding / SH3 domain binding / protein dimerization activity / DNA-binding transcription factor activity / DNA binding / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Corynebacterium diphtheriae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.4 Å | |||||||||
Authors | White, A. / Ding, X. / Zheng, H. / Schiering, N. / Ringe, D. / Murphy, J.R. | |||||||||
Citation | Journal: Nature / Year: 1998 Title: Structure of the metal-ion-activated diphtheria toxin repressor/tox operator complex. Authors: White, A. / Ding, X. / vanderSpek, J.C. / Murphy, J.R. / Ringe, D. #1: Journal: Nat.Struct.Biol. / Year: 1996 Title: Identification of the Primary Metal Ion-Activation Sites of the Diphtheria Tox Repressor by X-Ray Crystallography and Site-Directed Mutational Analysis Authors: Ding, X. / Zeng, H. / Schiering, N. / Ringe, D. / Murphy, J.R. #2: 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. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995 Title: Structures of the Apo-and the Metal Ion-Activated Forms of the Diphtheria Tox Repressor from Corynebacterium Diphtheriae Authors: Schiering, N. / Tao, X. / Zeng, H. / Murphy, J.R. / Petsko, G.A. / Ringe, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2tdx.cif.gz | 38.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2tdx.ent.gz | 28.5 KB | Display | PDB format |
PDBx/mmJSON format | 2tdx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/td/2tdx ftp://data.pdbj.org/pub/pdb/validation_reports/td/2tdx | HTTPS FTP |
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-Related structure data
Related structure data | 1ddnC 1dprS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25361.740 Da / Num. of mol.: 1 / Mutation: C102D Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH NICKEL (NI) / Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Gene: DTXR / Plasmid: PET11C / Production host: Escherichia coli (E. coli) / References: UniProt: P33120, UniProt: P0DJL7*PLUS | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.03 Å3/Da / Density % sol: 70 % | ||||||||||||||||||||||||||||||||||||
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Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jun 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→55 Å / Num. obs: 9464 / % possible obs: 80.6 % / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Rmerge(I) obs: 0.041 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: APO-DTXR (PDB ENTRY 1DPR) Resolution: 2.4→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 27 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.58 Å / Total num. of bins used: 5
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.3 |