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Yorodumi- PDB-1qd2: CRYSTAL STRUCTURE OF THE COMPLEX OF TRICHOSANTHIN WITH ADENINE, O... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qd2 | ||||||
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Title | CRYSTAL STRUCTURE OF THE COMPLEX OF TRICHOSANTHIN WITH ADENINE, OBTAINED FROM TRICHOSANTHIN COMPLEXED WITH THE DINUCLEOTIDE APG | ||||||
Components | TRICHOSANTHIN | ||||||
Keywords | HYDROLASE / ENZYME-PRODUCT COMPLEX OBTAINED FROM ENZYME-SUBSTRATE ANALOG COMPLEX | ||||||
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: 1.86 Å | ||||||
Authors | Gu, Y.J. / Xia, Z.X. | ||||||
Citation | Journal: Proteins / Year: 2000 Title: Crystal structures of the complexes of trichosanthin with four substrate analogs and catalytic mechanism of RNA N-glycosidase. Authors: Gu, Y.J. / Xia, Z.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qd2.cif.gz | 63.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qd2.ent.gz | 46.5 KB | Display | PDB format |
PDBx/mmJSON format | 1qd2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/1qd2 ftp://data.pdbj.org/pub/pdb/validation_reports/qd/1qd2 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar 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: 27166.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichosanthes kirilowii (gua lou) / References: UniProt: P09989, rRNA N-glycosylase |
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#2: Chemical | ChemComp-ADE / |
#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: 2.15 Å3/Da / Density % sol: 42.89 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 5 Details: HANGING DROP, CITRATE BUFFER, POTASSIUM CHLORIDE, DINUCLEOTIDE APG. NATIVE CRYSTALS SOAKED IN SOLUTION CONTAINING DINUCLEOTIDE APG, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 281K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SEALED TUBE / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→10 Å / Num. all: 20045 / Num. obs: 20045 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 11.25 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.86→1.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.343 / % possible all: 90.3 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 90.3 % |
-Processing
Software |
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Refinement | Resolution: 1.86→10 Å / σ(F): 2 / Stereochemistry target values: X-PLOR DICTIONARY
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Refinement step | Cycle: LAST / Resolution: 1.86→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |