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- PDB-3hio: Crystal structure of Ricin A-chain in complex with the cyclic tet... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3hio | ||||||
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Title | Crystal structure of Ricin A-chain in complex with the cyclic tetranucleotide inhibitor, a transition state analogue | ||||||
![]() | Ricin | ||||||
![]() | Hydrolase/Hydrolase inhibitor / RTA / transition state / ribosome inactivating proteins / RIPs / Disulfide bond / Glycoprotein / Hydrolase / Lectin / Nucleotide-binding / Plant defense / Protein synthesis inhibitor / Toxin / Hydrolase-Hydrolase inhibitor COMPLEX | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Ho, M. / Sturm, M.B. / Goldman, J.D. / Almo, S.C. / Schramm, V.L. | ||||||
![]() | ![]() Title: Transition state analogues in structures of ricin and saporin ribosome-inactivating proteins. Authors: Ho, M.C. / Sturm, M.B. / Almo, S.C. / Schramm, V.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.5 KB | Display | ![]() |
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PDB format | ![]() | 51 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 830.2 KB | Display | ![]() |
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Full document | ![]() | 840.7 KB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 18.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30067.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-C2X / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.11 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 25% PEG2000, 0.2M Lithium sulfate, 0.1M Sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.081 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→61.2 Å / Num. obs: 22257 / % possible obs: 98.9 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.059 / Χ2: 1.013 / Net I/σ(I): 30.077 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.27 Å2 / Biso mean: 21.98 Å2 / Biso min: 7.35 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.053 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -26.667 Å / Origin y: 14.935 Å / Origin z: 9.08 Å
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