+Open data
-Basic information
Entry | Database: PDB / ID: 3lc9 | ||||||
---|---|---|---|---|---|---|---|
Title | Ricin A-chain variant 1-33/44-198 with engineered disulfide bond | ||||||
Components | Ricin A chain | ||||||
Keywords | HYDROLASE / Ricin / disulfide bond / Nucleotide-binding / Plant defense / Protein synthesis inhibitor / Toxin / immunogen | ||||||
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: 2.28 Å | ||||||
Authors | Compton, J.R. / Legler, P.M. / Millard, C.B. | ||||||
Citation | Journal: Proteins / Year: 2011 Title: Introduction of a disulfide bond leads to stabilization and crystallization of a ricin immunogen. Authors: Compton, J.R. / Legler, P.M. / Clingan, B.V. / Olson, M.A. / Millard, C.B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3lc9.cif.gz | 49 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3lc9.ent.gz | 34.4 KB | Display | PDB format |
PDBx/mmJSON format | 3lc9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/3lc9 ftp://data.pdbj.org/pub/pdb/validation_reports/lc/3lc9 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3mk9C 3bjg S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 21415.188 Da / Num. of mol.: 1 / Mutation: R48C, T77C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ricinus communis (castor bean) / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3) / References: UniProt: P02879, rRNA N-glycosylase |
---|---|
#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.92 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: Protein buffer: 50mM MES pH 6.4, 200mM NaCl Crystallization Solution: 0.17M Ammonium Sulfate, 25.5% w/v PEG 4000, 15% v/v Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Aug 21, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→57.36 Å / Num. all: 8335 / Num. obs: 8333 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 16.01 % / Rsym value: 0.098 / Net I/σ(I): 19.05 |
Reflection shell | Resolution: 2.28→2.38 Å / Redundancy: 11.85 % / Mean I/σ(I) obs: 5.52 / Num. unique all: 979 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3BJG 3bjg Resolution: 2.28→57.36 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.901 / Cross valid method: THROUGHOUT / ESU R: 0.409 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 mean: 18.408 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.28→57.36 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.28→2.339 Å / Total num. of bins used: 20
|