+Open data
-Basic information
Entry | Database: PDB / ID: 1j4g | ||||||
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Title | crystal structure analysis of the trichosanthin delta C7 | ||||||
Components | Trichosanthin delta C7 | ||||||
Keywords | HYDROLASE / Antiviral / Protein synthesis inhibitor | ||||||
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: 2 Å | ||||||
Authors | Ding, Y. / Too, H.M. / Wang, Z.L. / Liu, Y.W. / Dong, Y.C. / Shaw, P.C. / Rao, Z.H. | ||||||
Citation | Journal: To be Published Title: crystal structure analysis of the trichosanthin delta C7 Authors: Ding, Y. / Too, H.M. / Wang, Z.L. / Liu, Y.W. / Dong, Y.C. / Shaw, P.C. / Rao, Z.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j4g.cif.gz | 213.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j4g.ent.gz | 170.5 KB | Display | PDB format |
PDBx/mmJSON format | 1j4g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/1j4g ftp://data.pdbj.org/pub/pdb/validation_reports/j4/1j4g | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 27297.965 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trichosanthes kirilowii (gua lou) / Plasmid: pET8c / Production host: Escherichia coli (E. coli) / References: UniProt: P09989, rRNA N-glycosylase #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.93 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: evaporation / pH: 6.5 Details: PEG8000, calcium acetate, sodium cacodylate, pH 6.5, EVAPORATION, temperature 291K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS 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: Jul 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: 2→30 Å / Num. all: 61794 / Num. obs: 59190 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2→2.13 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.225 / Num. unique all: 8268 / % possible all: 98.2 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 40 Å / Num. obs: 19310 / % possible obs: 98.2 % / Num. measured all: 61794 / Rmerge(I) obs: 0.071 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.87 Å / % possible obs: 95.8 % / Num. unique obs: 1950 / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 5.1 |
-Processing
Software |
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Refinement | Resolution: 2→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: CNS
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.174 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |