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Yorodumi- PDB-1bym: SOLUTION STRUCTURES OF THE C-TERMINAL DOMAIN OF DIPHTHERIA TOXIN ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bym | ||||||
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Title | SOLUTION STRUCTURES OF THE C-TERMINAL DOMAIN OF DIPHTHERIA TOXIN REPRESSOR | ||||||
Components | PROTEIN (DIPHTHERIA TOXIN REPRESSOR) | ||||||
Keywords | GENE REGULATION / REPRESSOR / DTXR / C-TERMINAL DOMAIN / PROKARYOTIC SH3 DOMAIN / TRANSCRIPTION REGULATION / PEPTIDE-BINDING | ||||||
Function / homology | Function and homology information 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 | Corynebacterium diphtheriae (bacteria) | ||||||
Method | SOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING CALCULATIONS | ||||||
Authors | Wang, G. / Wylie, G.P. / Twigg, P.D. / Caspar, D.L.D. / Murphy, J.R. / Logan, T.M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1999 Title: Solution structure and peptide binding studies of the C-terminal src homology 3-like domain of the diphtheria toxin repressor protein. Authors: Wang, G. / Wylie, G.P. / Twigg, P.D. / Caspar, D.L. / Murphy, J.R. / Logan, T.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bym.cif.gz | 580.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bym.ent.gz | 482.8 KB | Display | PDB format |
PDBx/mmJSON format | 1bym.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bym_validation.pdf.gz | 348.8 KB | Display | wwPDB validaton report |
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Full document | 1bym_full_validation.pdf.gz | 608.7 KB | Display | |
Data in XML | 1bym_validation.xml.gz | 71.8 KB | Display | |
Data in CIF | 1bym_validation.cif.gz | 94.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/1bym ftp://data.pdbj.org/pub/pdb/validation_reports/by/1bym | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 10609.798 Da / Num. of mol.: 1 / Fragment: RESIDUES 130-226 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Description: SWS P33120 / Gene: DTXR / Production host: Escherichia coli (E. coli) / Strain (production host): HMS-174 / References: UniProt: P33120, UniProt: P0DJL7*PLUS |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: IONIC_STRENGTH: NULL PRESSURE: NULL SOLVENT SYSTEM: H2O/D2O (9:1, V/V) |
-Sample preparation
Sample conditions | pH: 6.5 / Temperature: 303 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: DISTANCE GEOMETRY, SIMULATED ANNEALING CALCULATIONS / Software ordinal: 1 Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. | |||||||||
NMR ensemble | Conformer selection criteria: NO NOE DISTANCE VIOLATION GREATER THAN 0.35 A, NO DIHEDRAL ANGLE RESTRAINT VIOLATION GREATER THAN 5 DEG, RMS DIFFERENCE FOR BOND DEVIATIONS FROM IDEALITY LESS THAN 0.01 ...Conformer selection criteria: NO NOE DISTANCE VIOLATION GREATER THAN 0.35 A, NO DIHEDRAL ANGLE RESTRAINT VIOLATION GREATER THAN 5 DEG, RMS DIFFERENCE FOR BOND DEVIATIONS FROM IDEALITY LESS THAN 0.01 A, RMS DIFFERENCE FOR ANGLE DEVIATIONS FROM IDEALITY LESS THAN 2 DEG, LOWEST TOTAL ENERGY Conformers calculated total number: 100 / Conformers submitted total number: 20 |