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Open data
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Basic information
Entry | Database: PDB / ID: 2tdx | |||||||||
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Title | DIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL | |||||||||
![]() | DIPHTHERIA TOX REPRESSOR | |||||||||
![]() | DNA BINDING PROTEIN / DNA-BINDING REGULATORY PROTEIN / DIPHTHERIA TOX REPRESSOR / TRANSCRIPTION REGULATION / DNA-BINDING PROTEIN / IRON-REGULATED REPRESSOR | |||||||||
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 | ![]() | |||||||||
![]() | White, A. / Ding, X. / Zheng, H. / Schiering, N. / Ringe, D. / Murphy, J.R. | |||||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 42.1 KB | Display | ![]() |
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PDB format | ![]() | 28.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 367.5 KB | Display | ![]() |
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Full document | ![]() | 373.1 KB | Display | |
Data in XML | ![]() | 5 KB | Display | |
Data in CIF | ![]() | 6.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ddnC ![]() 1dprS S: Starting model for refinement C: citing same article ( |
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Similar 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: 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.) ![]() ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() |
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 |
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Processing
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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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.3 |