+Open data
-Basic information
Entry | Database: PDB / ID: 2aai | |||||||||
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Title | Crystallographic refinement of ricin to 2.5 Angstroms | |||||||||
Components |
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Keywords | HYDROLASE / GLYCOSIDASE | |||||||||
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: 2.5 Å | |||||||||
Authors | Rutenber, E. / Katzin, B.J. / Montfort, W. / Villafranca, J.E. / Ernst, S.R. / Collins, E.J. / Mlsna, D. / Monzingo, A.F. / Ready, M.P. / Robertus, J.D. | |||||||||
Citation | Journal: Proteins / Year: 1991 Title: Crystallographic refinement of ricin to 2.5 A. Authors: Rutenber, E. / Katzin, B.J. / Ernst, S. / Collins, E.J. / Mlsna, D. / Ready, M.P. / Robertus, J.D. #1: Journal: Proteins / Year: 1991 Title: Structure of Ricin A-Chain at 2.5 Angstroms Authors: Katzin, B.J. / Collins, E.J. / Robertus, J.D. #2: Journal: Proteins / Year: 1991 Title: Structure of Ricin B-Chain at 2.5 Angstroms Authors: Rutenber, E. / Robertus, J.D. #3: Journal: J.Biol.Chem. / Year: 1987 Title: The Three-Dimensional Structure of Ricin at 2.8 Angstroms Authors: Montfort, W. / Villafranca, J.E. / Monzingo, A.F. / Ernst, S.R. / Katzin, B. / Rutenber, E. / Xuong, N.H. / Hamlin, R. / 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 | 2aai.cif.gz | 118.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2aai.ent.gz | 94.6 KB | Display | PDB format |
PDBx/mmJSON format | 2aai.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/2aai ftp://data.pdbj.org/pub/pdb/validation_reports/aa/2aai | 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: RESIDUE PRO A 263 DEVIATED SIGNIFICANTLY FROM THE TRANS CONFORMATION. |
-Components
#1: Protein | Mass: 29936.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ricinus communis (castor bean) / References: UniProt: P02879, rRNA N-glycosylase | ||||
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#2: Protein | Mass: 28989.580 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source References: UniProt: P02879, rRNA N-glycosylase | ||||
#3: Polysaccharide | #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.57 % |
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Crystal grow | *PLUS Method: other / Details: unknown |
-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 5 Å / Num. obs: 18572 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.212 / Rfactor obs: 0.212 / Highest resolution: 2.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.5 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 5 Å / Rfactor obs: 0.212 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 4.13 |