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Yorodumi- PDB-1il9: STRUCTURE OF RICIN A CHAIN BOUND WITH INHIBITOR 8-METHYL-9-OXOGUANINE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1il9 | ||||||
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Title | STRUCTURE OF RICIN A CHAIN BOUND WITH INHIBITOR 8-METHYL-9-OXOGUANINE | ||||||
Components | RICIN A CHAIN | ||||||
Keywords | HYDROLASE / STRUCTURE-BASED DESIGN / TOXIN-INHIBITOR COMPLEX / GLYCOSIDASE / RIBOSOME-INHIBITING PROTEIN | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Miller, D.J. / Ravikumar, K. / Shen, H. / Suh, J.-K. / Kerwin, S.M. / Robertus, J.D. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2002 Title: Structure-based design and characterization of novel platforms for ricin and shiga toxin inhibition. Authors: Miller, D.J. / Ravikumar, K. / Shen, H. / Suh, J.K. / Kerwin, S.M. / 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 | 1il9.cif.gz | 62.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1il9.ent.gz | 44.9 KB | Display | PDB format |
PDBx/mmJSON format | 1il9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1il9_validation.pdf.gz | 443.3 KB | Display | wwPDB validaton report |
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Full document | 1il9_full_validation.pdf.gz | 447.7 KB | Display | |
Data in XML | 1il9_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 1il9_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/il/1il9 ftp://data.pdbj.org/pub/pdb/validation_reports/il/1il9 | HTTPS FTP |
-Related structure data
Related structure data | 1il3C 1il4C 1il5C 1rtcS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 29936.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ricinus communis (castor bean) / Production host: Escherichia coli (E. coli) / References: UniProt: P02879, rRNA N-glycosylase |
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#2: Chemical | ChemComp-MOG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.71 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.9 Details: PEG 8000, TRIS-HCL, BETA-MERCAPTOETHANOL, EDTA, 8-METHYL-9-OXOGUANINE, pH 8.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Mlsna, D., (1993) Protein Sci., 2, 429. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 17, 2000 |
Radiation | Monochromator: DOUBLE FOCUSSING MIRRORS (NI & PT) + NI FILTER Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→20 Å / Num. obs: 5350 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 2.82 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 10.15 |
Reflection shell | Resolution: 3.1→3.2 Å / Rmerge(I) obs: 0.1592 / % possible all: 95.4 |
Reflection | *PLUS Num. measured all: 15067 |
Reflection shell | *PLUS % possible obs: 95.4 % / Mean I/σ(I) obs: 4.08 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RTC Resolution: 3.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 3.1→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3.1 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 6 % / Rfactor obs: 0.247 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |