+Open data
-Basic information
Entry | Database: PDB / ID: 1giu | ||||||
---|---|---|---|---|---|---|---|
Title | A TRICHOSANTHIN(TCS) MUTANT(E85R) COMPLEX STRUCTURE WITH ADENINE | ||||||
Components | RIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN | ||||||
Keywords | HYDROLASE / PROTEIN-SUB COMPLEX / TRICHOSANTHIN / TCS | ||||||
Function / homology | Function and homology information regulation of defense response to virus / rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / toxin activity / negative regulation of translation Similarity search - Function | ||||||
Biological species | Trichosanthes kirilowii (gua lou) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Guo, Q. / Liu, Y. / Dong, Y. / Rao, Z. | ||||||
Citation | Journal: Protein Eng. / Year: 2003 Title: Substrate binding and catalysis in trichosanthin occur in different sites as revealed by the complex structures of several E85 mutants. Authors: Guo, Q. / Zhou, W. / Too, H.M. / Li, J. / Liu, Y. / Bartlam, M. / Dong, Y. / Wong, K.B. / Shaw, P.C. / Rao, Z. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1giu.cif.gz | 63.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1giu.ent.gz | 47 KB | Display | PDB format |
PDBx/mmJSON format | 1giu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1giu_validation.pdf.gz | 386.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1giu_full_validation.pdf.gz | 394.4 KB | Display | |
Data in XML | 1giu_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 1giu_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/1giu ftp://data.pdbj.org/pub/pdb/validation_reports/gi/1giu | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 27194.850 Da / Num. of mol.: 1 / Mutation: E85R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trichosanthes kirilowii (gua lou) / Production host: Escherichia coli (E. coli) / References: UniProt: P09989, rRNA N-glycosylase |
---|---|
#2: Chemical | ChemComp-ADE / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.34 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 291 K / Method: evaporation / pH: 5.7 Details: CaCl2, KCl, NaAC-HAC, pH 5.7, EVAPORATION, temperature 291.0K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 K / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 29, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 21505 / Num. obs: 21401 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 8.7 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.517 / Num. unique all: 2062 / % possible all: 99.2 |
Reflection | *PLUS Lowest resolution: 50 Å |
Reflection shell | *PLUS % possible obs: 99.2 % |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.8→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: CNS
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor obs: 0.21 / Rfactor Rwork: 0.21 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |