+Open data
-Basic information
Entry | Database: PDB / ID: 1uq4 | ||||||
---|---|---|---|---|---|---|---|
Title | RICIN A-CHAIN (RECOMBINANT) R213D MUTANT | ||||||
Components | RICIN | ||||||
Keywords | HYDROLASE / GLYCOSIDASE / TOXIN / GLYCOPROTEIN | ||||||
Function / homology | Function and homology information rRNA N-glycosylase / rRNA N-glycosylase activity / AMP binding / defense response / carbohydrate binding / toxin activity / 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: 1.9 Å | ||||||
Authors | Marsden, C.J. / Fulop, V. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 2004 Title: The Effect of Mutations Surrounding and within the Active Site on the Catalytic Activity of Ricin a Chain Authors: Marsden, C.J. / Fulop, V. / Day, P. / Lord, J.M. #1: Journal: J.Mol.Biol. / Year: 1994 Title: X-Ray Structure of Recombinant Ricin A-Chain at 1.8 A Resolution Authors: Weston, S.A. / Tucker, A.D. / Thatcher, D.R. / Derbyshire, D.J. / Pauptit, R.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1uq4.cif.gz | 75.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1uq4.ent.gz | 55.2 KB | Display | PDB format |
PDBx/mmJSON format | 1uq4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uq4_validation.pdf.gz | 432.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1uq4_full_validation.pdf.gz | 434.4 KB | Display | |
Data in XML | 1uq4_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 1uq4_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uq/1uq4 ftp://data.pdbj.org/pub/pdb/validation_reports/uq/1uq4 | HTTPS FTP |
-Related structure data
Related structure data | 1uq5C 1iftS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
| ||||||||||||
Details | THIS DIMER IS BECAUSE OF CRYSTAL PACKING BUT NONETHELESSGIVES AN INTERESTING RESULT |
-Components
#1: Protein | Mass: 29408.029 Da / Num. of mol.: 1 / Fragment: A CHAIN, RESIDUES 40-302 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) RICINUS COMMUNIS (castor bean) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM101 / References: UniProt: P02879, rRNA N-glycosylase | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 48 % | |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 4.2 / Details: SEE REFERENCE 1, pH 4.20 | |||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8.9 / Method: vapor diffusion, hanging drop / Details: Weston, S.A., (1994) J. Mol. Biol., 244, 410. | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
Detector | Type: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Nov 17, 2000 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→28 Å / Num. obs: 53233 / % possible obs: 86 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.133 / Mean I/σ(I) obs: 4.7 / % possible all: 44 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 28 Å / Num. obs: 22494 / % possible obs: 85.6 % / Num. measured all: 53233 / Rmerge(I) obs: 0.038 |
Reflection shell | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 1.949 Å / % possible obs: 43.6 % / Rmerge(I) obs: 0.133 / Mean I/σ(I) obs: 4.7 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IFT Resolution: 1.9→28 Å / SU B: 3.03 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.159
| ||||||||||||||||||||
Displacement parameters | Biso mean: 24.8 Å2
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→28 Å
| ||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 4 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.257 / Num. reflection Rfree: 24 / Rfactor Rwork: 0.154 / Num. reflection Rwork: 720 |