+Open data
-Basic information
Entry | Database: PDB / ID: 1obt | ||||||
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Title | STRUCTURE OF RICIN A CHAIN MUTANT, COMPLEX WITH AMP | ||||||
Components | RICIN A CHAIN | ||||||
Keywords | GLYCOSIDASE / HYDROLASE / TOXIN / DUPLICATION / GLYCOPROTEIN / LECTIN | ||||||
Function / homology | Function and homology information rRNA N-glycosylase / rRNA N-glycosylase activity / AMP binding / defense response / toxin activity / carbohydrate binding / killing of cells of another organism / negative regulation of translation Similarity search - Function | ||||||
Biological species | Ricinus communis (castor bean) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | ||||||
Authors | Day, P.J. / Ernst, S.R. / Frankel, A.E. / Monzingo, A.F. / Pascal, J.M. / Svinth, M. / Robertus, J.D. | ||||||
Citation | Journal: Biochemistry / Year: 1996 Title: Structure and activity of an active site substitution of ricin A chain. Authors: Day, P.J. / Ernst, S.R. / Frankel, A.E. / Monzingo, A.F. / Pascal, J.M. / Molina-Svinth, M.C. / Robertus, J.D. #1: Journal: J.Mol.Biol. / Year: 1994 Title: X-Ray Structure of Recombinant Ricin A-Chain at 1.8 A Resolution Authors: Weston, S.A. / Tucker, A.D. / Thatcher, D.R. / Derbyshire, D.J. / Pauptit, R.A. #2: Journal: Protein Sci. / Year: 1993 Title: Structure of Recombinant Ricin a Chain at 2.3 A Authors: Mlsna, D. / Monzingo, A.F. / Katzin, B.J. / Ernst, S. / Robertus, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1obt.cif.gz | 65.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1obt.ent.gz | 47.8 KB | Display | PDB format |
PDBx/mmJSON format | 1obt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/1obt ftp://data.pdbj.org/pub/pdb/validation_reports/ob/1obt | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29917.711 Da / Num. of mol.: 1 / Mutation: R180H Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH AMP / Source: (gene. exp.) Ricinus communis (castor bean) / Plasmid: PUTA / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P02879, rRNA N-glycosylase |
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#2: Chemical | ChemComp-AMP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Feb 16, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 23545 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 13 % / Rmerge(I) obs: 0.069 |
-Processing
Software |
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Refinement | Resolution: 2.8→10 Å / σ(F): 2 Details: SET OF IDEAL BOND LENGTHS AND ANGLES USED DURING REFINEMENT: RAMACHANDRAN ET AL. (1974), BIOCHIM. BIOPHYS. ACTA 359, 298. FINAL RMS COORD. SHIFT 0.52 ANGSTROMS
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Displacement parameters | Biso mean: 21.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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