+Open data
-Basic information
Entry | Database: PDB / ID: 1ift | ||||||
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Title | RICIN A-CHAIN (RECOMBINANT) | ||||||
Components | RICIN | ||||||
Keywords | HYDROLASE / GLYCOSIDASE / TOXIN / GLYCOPROTEIN | ||||||
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: 1.8 Å | ||||||
Authors | Weston, S.A. / Tucker, A.D. / Thatcher, D.R. / Derbyshire, D.J. / Pauptit, R.A. | ||||||
Citation | 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ift.cif.gz | 63.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ift.ent.gz | 47 KB | Display | PDB format |
PDBx/mmJSON format | 1ift.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/1ift ftp://data.pdbj.org/pub/pdb/validation_reports/if/1ift | 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: 29457.291 Da / Num. of mol.: 1 / Fragment: A CHAIN / Mutation: I1M, F2V 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: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.57 % | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8.9 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||
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 | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 14.8 Å / Num. obs: 26549 / % possible obs: 90.4 % / Rmerge(I) obs: 0.075 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / % possible obs: 86.3 % / Rmerge(I) obs: 0.504 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.216 / Rfactor obs: 0.216 / Highest resolution: 1.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.8 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 14.8 Å / Rfactor obs: 0.186 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 0.18 Å / Lowest resolution: 0.19 Å / Rfactor all: 0.35 |