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Open data
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Basic information
Entry | Database: PDB / ID: 1ddn | ||||||
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Title | DIPHTHERIA TOX REPRESSOR (C102D MUTANT)/TOX DNA OPERATOR COMPLEX | ||||||
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![]() | GENE REGULATION/DNA / COMPLEX (REGULATORY PROTEIN-DNA) / DIPHTHERIA TOX REPRESSOR / TRANSCRIPTION REGULATION / DNA-BINDING REGULATORY PROTEIN / IRON-REGULATED REPRESSOR / DNA- PROTEIN / DNA-REPRESSOR COMPLEX / GENE REGULATION-DNA COMPLEX | ||||||
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. / Vanderspek, J.C. / Murphy, J.R. / Ringe, D. | ||||||
![]() | ![]() 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: 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. #3: ![]() Title: Cysteine-102 is Positioned in the Metal Binding Activation Site of the Corynebacterium Diphtheriae Regulatory Element Dtxr Authors: Tao, X. / Murphy, J.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 132.5 KB | Display | ![]() |
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PDB format | ![]() | 102.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 409.8 KB | Display | ![]() |
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Full document | ![]() | 442 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 23.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2tdxC ![]() 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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Unit cell |
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Components
#1: DNA chain | Mass: 10131.578 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
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#2: DNA chain | Mass: 10158.620 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
#3: Protein | Mass: 25361.740 Da / Num. of mol.: 4 / Mutation: C102D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Chemical | ChemComp-NI / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.07 Å3/Da / Density % sol: 69.76 % | ||||||||||||||||||||||||||||||||||||
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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: BRANDEIS / Detector: CCD / Date: Feb 15, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. all: 32605 / Num. obs: 32605 / % possible obs: 87.4 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 7.6 |
Reflection | *PLUS Num. obs: 34176 / Num. measured all: 107910 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DPR Resolution: 3→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→8 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.22 Å / Total num. of bins used: 5
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.24 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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