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Open data
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Basic information
Entry | Database: PDB / ID: 1il3 | ||||||
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Title | STRUCTURE OF RICIN A CHAIN BOUND WITH INHIBITOR 7-DEAZAGUANINE | ||||||
![]() | RICIN A CHAIN | ||||||
![]() | HYDROLASE / STRUCTURE-BASED DESIGN / TOXIN-INHIBITOR COMPLEX / GLYCOSIDASE / RIBOSOME-INHIBITING PROTEIN | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Miller, D.J. / Ravikumar, K. / Shen, H. / Suh, J.-K. / Kerwin, S.M. / Robertus, J.D. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.2 KB | Display | ![]() |
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PDB format | ![]() | 47.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.9 KB | Display | ![]() |
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Full document | ![]() | 443.9 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 15.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1il4C ![]() 1il5C ![]() 1il9C ![]() 1rtcS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-7DG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.14 % | ||||||||||||||||||||||||||||||||||||
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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, 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: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 24, 1999 |
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: 2.8→20 Å / Num. all: 6621 / Num. obs: 6621 / % possible obs: 94.7 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 9.93 |
Reflection shell | Resolution: 2.8→2.89 Å / Redundancy: 1.67 % / Rmerge(I) obs: 0.192 / % possible all: 93.5 |
Reflection | *PLUS Num. measured all: 12592 / Rmerge(I) obs: 0.071 |
Reflection shell | *PLUS % possible obs: 93.5 % / Mean I/σ(I) obs: 3.57 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1RTC Resolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5.5 % / Rfactor obs: 0.202 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |