+Open data
-Basic information
Entry | Database: PDB / ID: 1ddn | ||||||
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Title | DIPHTHERIA TOX REPRESSOR (C102D MUTANT)/TOX DNA OPERATOR COMPLEX | ||||||
Components |
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Keywords | 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 | 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | White, A. / Ding, X. / Vanderspek, J.C. / Murphy, J.R. / Ringe, D. | ||||||
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: 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. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ddn.cif.gz | 132.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ddn.ent.gz | 102.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ddn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/1ddn ftp://data.pdbj.org/pub/pdb/validation_reports/dd/1ddn | HTTPS FTP |
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-Related structure data
Related structure data | 2tdxC 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: 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.) Corynebacterium diphtheriae (bacteria) / Gene: DTXR / Plasmid: PET11C / Production host: Escherichia coli (E. coli) / References: UniProt: P33120, UniProt: P0DJL7*PLUS #4: Chemical | ChemComp-NI / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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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: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.24 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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