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Yorodumi- PDB-1gis: A TRICHOSANTHIN(TCS) MUTANT(E85Q) COMPLEX STRUCTURE WITH 2'-DEOXY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gis | ||||||
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Title | A TRICHOSANTHIN(TCS) MUTANT(E85Q) COMPLEX STRUCTURE WITH 2'-DEOXY-ADENOSIN-5'-MONOPHOSPHATE | ||||||
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: 1.7 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gis.cif.gz | 68.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gis.ent.gz | 49.4 KB | Display | PDB format |
PDBx/mmJSON format | 1gis.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/1gis ftp://data.pdbj.org/pub/pdb/validation_reports/gi/1gis | HTTPS FTP |
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-Related 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: 27296.980 Da / Num. of mol.: 1 / Mutation: E86Q 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 |
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#2: Chemical | ChemComp-DA / |
#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: 2.07 Å3/Da / Density % sol: 40.59 % | |||||||||||||||||||||||||||||||||||
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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
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 28, 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: 1.7→50 Å / Num. all: 25659 / Num. obs: 24510 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.236 / Num. unique all: 2392 / % possible all: 95.6 |
Reflection | *PLUS Lowest resolution: 50 Å |
Reflection shell | *PLUS % possible obs: 95.6 % |
-Processing
Software |
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Refinement | Resolution: 1.7→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: CNS
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Refinement step | Cycle: LAST / Resolution: 1.7→50 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 30 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |