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Yorodumi- PDB-1aha: THE N-GLYCOSIDASE MECHANISM OF RIBOSOME-INACTIVATING PROTEINS IMP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1aha | ||||||
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Title | THE N-GLYCOSIDASE MECHANISM OF RIBOSOME-INACTIVATING PROTEINS IMPLIED BY CRYSTAL STRUCTURES OF ALPHA-MOMORCHARIN | ||||||
Components | ALPHA-MOMORCHARIN | ||||||
Keywords | GLYCOSIDASE | ||||||
Function / homology | Function and homology information rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / toxin activity / negative regulation of translation Similarity search - Function | ||||||
Biological species | Momordica charantia (bitter melon) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Ren, J. / Wang, Y. / Dong, Y. / Stuart, D.I. | ||||||
Citation | Journal: Structure / Year: 1994 Title: The N-glycosidase mechanism of ribosome-inactivating proteins implied by crystal structures of alpha-momorcharin. Authors: Ren, J. / Wang, Y. / Dong, Y. / Stuart, D.I. #1: Journal: Daresbury Lab.[Rep.]Dl/Sci/R / Year: 1992 Title: Molecular Replacement Studies of Alpha-Momorcharin (in: Proceedings of the Ccp4 Study Weekend: Molecular Replacement, Edited by E.J.Dodson, S.Gover,W.Wolf) Authors: Ren, J. / Wang, Y. / Dong, Y. / Stuart, D.I. #2: Journal: J.Mol.Biol. / Year: 1990 Title: Crystals of Alpha-Momorcharin, a New Ribosome-Inactivating Protein Authors: Feng, Z. / Li, W.W. / Yeung, H.W. / Chen, S. / Wang, Y. / Lin, X. / Dong, Y. / Wang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1aha.cif.gz | 61.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1aha.ent.gz | 45.5 KB | Display | PDB format |
PDBx/mmJSON format | 1aha.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/1aha ftp://data.pdbj.org/pub/pdb/validation_reports/ah/1aha | 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: 27396.285 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Momordica charantia (bitter melon) / References: UniProt: P16094, rRNA N-glycosylase |
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#2: Chemical | ChemComp-ADE / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.25 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.65 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 100 Å / Num. obs: 9071 / % possible obs: 84.4 % / Observed criterion σ(I): 3 / Num. measured all: 10629 / Rmerge(I) obs: 0.087 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.5 Å / % possible obs: 58.5 % / Num. unique obs: 1499 / Num. measured obs: 2352 / Rmerge(I) obs: 0.151 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.183 / Rfactor obs: 0.183 / Highest resolution: 2.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.2 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / Rfactor obs: 0.183 / Rfactor Rwork: 0.183 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.83 |