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- PDB-1aqz: CRYSTAL STRUCTURE OF A HIGHLY SPECIFIC ASPERGILLUS RIBOTOXIN, RES... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1aqz | ||||||
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Title | CRYSTAL STRUCTURE OF A HIGHLY SPECIFIC ASPERGILLUS RIBOTOXIN, RESTRICTOCIN | ||||||
![]() | RESTRICTOCIN | ||||||
![]() | RIBOTOXIN / RIBOSOME-INACTIVATING PROTEIN / PROTEIN-RNA SPECIFIC INTERACTION / LAUE DIFFRACTION / CELL-ENTRY ACTIVITY | ||||||
Function / homology | ![]() Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA nuclease activity / negative regulation of translation / RNA binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Yang, X. / Moffat, K. | ||||||
![]() | ![]() Title: Insights into specificity of cleavage and mechanism of cell entry from the crystal structure of the highly specific Aspergillus ribotoxin, restrictocin. Authors: Yang, X. / Moffat, K. #1: ![]() Title: The Conformation of the Sarcin/Ricin Loop from 28S Ribosomal RNA Authors: Szewczak, A.A. / Moore, P.B. / Chan, Y.L. / Wool, I.G. #2: ![]() Title: Determination and Restrained Least-Squares Refinement of the Structures of Ribonuclease Sa and its Complex with 3'-Guanylic Acid at 1.8 A Resolution Authors: Sevcik, J. / Dodson, E.J. / Dodson, G.G. #3: ![]() Title: Crystallization and Preliminary Characterization of Mitogillin, a Ribosomal Ribonuclease from Aspergillus Restrictus Authors: Martinez, S.E. / Smith, J.L. #4: ![]() Title: The Mechanism of Action of the Cytotoxic Nuclease Alpha-Sarcin and its Use to Analyse Ribosome Structure Authors: Wool, I.G. #5: ![]() Title: Specific Protein-Nucleic Acid Recognition in Ribonuclease T1-2'-Guanylic Acid Complex: An X-Ray Study Authors: Heinemann, U. / Saenger, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.5 KB | Display | ![]() |
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PDB format | ![]() | 56.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.996739, 0.022599, -0.077458), Vector: |
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Components
#1: Protein | Mass: 16888.893 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: INORGANIC PHOSPHATE GROUP AT THE ACTIVE SITE / Source: (natural) ![]() ![]() References: UniProt: P67876, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46 % Description: DATA WERE COLLECTED USING LAUE DIFFRACTION. 62 IMAGES WERE COLLECTED. TOTAL EXPOSURE TIME IS 325 MS. | ||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, microdialysis / pH: 6.8 Details: A COMBINATION OF VAPOR DIFFUSION AND MICRODIALYSIS TECHNIQUES WERE USED TO CRYSTALLIZE RESTRICTOCIN. THE FINAL MOTHER LIQUOR CONSISTS OF 60% ETHANOL, 10MM SODIUM PHOSPHATE, PH6.8. THE ...Details: A COMBINATION OF VAPOR DIFFUSION AND MICRODIALYSIS TECHNIQUES WERE USED TO CRYSTALLIZE RESTRICTOCIN. THE FINAL MOTHER LIQUOR CONSISTS OF 60% ETHANOL, 10MM SODIUM PHOSPHATE, PH6.8. THE PROTEIN CONCENTRATION IS 10MG/ML., vapor diffusion and microdialysis | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Aug 1, 1994 / Details: MIRROR | |||||||||
Radiation | Monochromatic (M) / Laue (L): L / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→8 Å / Num. obs: 28328 / % possible obs: 85.6 % / Observed criterion σ(I): 2 / Redundancy: 8 % / Rmerge(I) obs: 0.039 | |||||||||
Reflection shell | Resolution: 1.7→1.78 Å / % possible all: 54.8 |
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Processing
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Refinement | Method to determine structure: SINGLE ISOMORPHOUS REPLACEMENT, ANOMALOUS SCATTERING Resolution: 1.7→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 19.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.78 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.177 / Rfactor Rfree: 0.237 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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