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Yorodumi- PDB-1dpr: STRUCTURES OF THE APO-AND METAL ION ACTIVATED FORMS OF THE DIPHTH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dpr | ||||||
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Title | STRUCTURES OF THE APO-AND METAL ION ACTIVATED FORMS OF THE DIPHTHERIA TOX REPRESSOR FROM CORYNEBACTERIUM DIPHTHERIAE | ||||||
Components | DIPHTHERIA TOX REPRESSOR | ||||||
Keywords | TRANSCRIPTION REGULATION / DIPHTHERIA / VIRULENCE / DNA-BINDING / IRON-REGULATION 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 / Resolution: 3 Å | ||||||
Authors | Schiering, N. / Tao, X. / Murphy, J. / Petsko, G.A. / Ringe, D. | ||||||
Citation | 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. #1: Journal: Mol.Microbiol. / Year: 1994 Title: Iron, Dtxr, and the Regulation of Diphtheria Toxin Expression Authors: Tao, X. / Schiering, N. / Zeng, H. / Ringe, D. / Murphy, J. #2: Journal: J.Mol.Biol. / Year: 1994 Title: Crystallization and Preliminary X-Ray Studies of the Diphtheria Tox Repressor from Corynebacterium Diphtheriae Authors: Schiering, N. / Tao, X. / Murphy, J. / Petsko, G. / Ringe, D. | ||||||
History |
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Remark 650 | HELIX HELIX DETERMINATION METHOD: DSSP AND O. | ||||||
Remark 700 | SHEET SHEET SHEET_ID: 1; DETERMINATION METHOD: DSSP AND O. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dpr.cif.gz | 62.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dpr.ent.gz | 45.7 KB | Display | PDB format |
PDBx/mmJSON format | 1dpr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/1dpr ftp://data.pdbj.org/pub/pdb/validation_reports/dp/1dpr | HTTPS FTP |
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-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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Atom site foot note | 1: GLY B 38 - PRO B 39 OMEGA = 144.51 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.507, 0.861, 0.032), Vector: Details | MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 3 .. A 136 B 3 .. B 136 1.491 | |
-Components
#1: Protein | Mass: 25349.795 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Strain: C7(-) / Plasmid: PDR1 / Production host: Escherichia coli (E. coli) / References: UniProt: P33120, UniProt: P0DJL7*PLUS |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.13 % | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop / Details: Schiering, N., (1994) J.Mol.Biol., 244, 654. | ||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Num. obs: 9355 / % possible obs: 83.8 % |
Reflection | *PLUS Highest resolution: 3 Å / Num. measured all: 21855 / Rmerge(I) obs: 0.075 |
-Processing
Software |
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Refinement | Resolution: 3→8 Å / σ(F): 2
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Displacement parameters | Biso mean: 13.98 Å2 | ||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.4 Å | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→8 Å
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Software | *PLUS Version: 3.1 / Classification: refinement | ||||||||||||
Refinement | *PLUS Num. reflection obs: 7378 / Rfactor obs: 0.233 / Rfactor Rfree: 0.413 / Rfactor Rwork: 0.233 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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