+Open data
-Basic information
Entry | Database: PDB / ID: 1br5 | ||||||
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Title | RICIN A CHAIN (RECOMBINANT) COMPLEX WITH NEOPTERIN | ||||||
Components | PROTEIN (RICIN) | ||||||
Keywords | HYDROLASE / GLYCOSIDASE | ||||||
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 / OTHER / Resolution: 2.5 Å | ||||||
Authors | Day, P. / Yan, X. / Hollis, T. / Svinth, M. / Monzingo, A.F. / Milne, G.W.A. / Robertus, J.D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1997 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: Journal: Protein Sci. / Year: 1993 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: Journal: Proteins / Year: 1991 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1br5.cif.gz | 66.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1br5.ent.gz | 48.2 KB | Display | PDB format |
PDBx/mmJSON format | 1br5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1br5_validation.pdf.gz | 717.8 KB | Display | wwPDB validaton report |
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Full document | 1br5_full_validation.pdf.gz | 725.2 KB | Display | |
Data in XML | 1br5_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 1br5_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/1br5 ftp://data.pdbj.org/pub/pdb/validation_reports/br/1br5 | HTTPS FTP |
-Related structure data
Related structure data | 1br6C 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) / Organ: SEED / Production host: Escherichia coli (E. coli) / References: UniProt: P02879, rRNA N-glycosylase |
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#2: Chemical | ChemComp-NEO / |
#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: 2.25 Å3/Da / Density % sol: 45.8 % | |||||||||||||||||||||||||
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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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Dec 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: 2.24→20 Å / Num. obs: 11996 / % possible obs: 92 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.0717 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.24→2.41 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 2.3 / % possible all: 75 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: PDB ENTRY 1RTC Resolution: 2.5→10 Å / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / σ(F): 2
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Refine analyze | Luzzati d res low obs: 0 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.61 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 10 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.242 |