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Open data
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Basic information
Entry | Database: PDB / ID: 1br6 | ||||||
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Title | RICIN A CHAIN (RECOMBINANT) COMPLEX WITH PTEROIC ACID | ||||||
![]() | PROTEIN (RICIN) | ||||||
![]() | HYDROLASE / GLYCOSIDASE | ||||||
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 | ![]() ![]() | ||||||
![]() | Hollis, T. / Yan, X. / Svinth, M. / Day, P. / Monzingo, A.F. / Milne, G.W.A. / Robertus, J.D. | ||||||
![]() | ![]() Title: Structure-based identification of a ricin inhibitor. Authors: Yan, X. / Hollis, T. / Svinth, M. / Day, P. / Monzingo, A.F. / Milne, G.W. / Robertus, J.D. #1: ![]() Title: The Structure of Recombinant Ricin a Chain at 2.3 Angstroms Authors: Mlsna, D. / Monzingo, A.F. / Katzin, B.J. / Ernst, S. / Robertus, J.D. #2: ![]() Title: Structure of Ricin A-Chain at 2.5 Angstroms Authors: Katzin, B.J. / Collins, E.J. / 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 | ![]() | 67.1 KB | Display | ![]() |
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PDB format | ![]() | 48.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 730.4 KB | Display | ![]() |
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Full document | ![]() | 740 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 17.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1br5C ![]() 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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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-PT1 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 37.3 % | |||||||||||||||||||||||||
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Crystal grow | pH: 8.9 / Details: pH 8.9 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Robertus, J.D., (1987) J. Biol. Chem., 262, 19. | |||||||||||||||||||||||||
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: SDMS / Detector: AREA DETECTOR / Date: Aug 15, 1995 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→20 Å / Num. obs: 10999 / % possible obs: 96 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.0612 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.23→2.4 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.135 / Mean I/σ(I) obs: 4.2 / % possible all: 78 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1RTC Resolution: 2.3→5 Å / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / σ(F): 0
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Refine analyze | Luzzati d res low obs: 0 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.39 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 5 Å / σ(F): 0 / Rfactor obs: 0.18 / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.224 |