+Open data
-Basic information
Entry | Database: PDB / ID: 1dy5 | ||||||
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Title | Deamidated derivative of bovine pancreatic ribonuclease | ||||||
Components | RIBONUCLEASE A | ||||||
Keywords | HYDROLASE / RIBONUCLEASE / DEAMIDATION | ||||||
Function / homology | Function and homology information pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region Similarity search - Function | ||||||
Biological species | BOS TAURUS (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.87 Å | ||||||
Authors | Esposito, L. / Vitagliano, L. / Sica, F. / Zagari, A. / Mazzarella, L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: The Ultrahigh Resolution Crystal Structure of Ribonuclease A Containing an Isoaspartyl Residue: Hydration and Sterochemical Analysis. Authors: Esposito, L. / Vitagliano, L. / Sica, F. / Sorrentino, G. / Zagari, A. / Mazzarella, L. #1: Journal: J.Mol.Biol. / Year: 1996 Title: Deamidation in Proteins:The Crystal Structure of Bovine Pancreatic Ribonuclease with an Isoaspartyl Residue at Position 67 Authors: Capasso, S. / Di Donato, A. / Esposito, L. / Sica, F. / Sorrentino, G. / Vitagliano, L. / Zagari, A. / Mazzarella, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dy5.cif.gz | 200 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dy5.ent.gz | 158.7 KB | Display | PDB format |
PDBx/mmJSON format | 1dy5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dy5_validation.pdf.gz | 452.5 KB | Display | wwPDB validaton report |
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Full document | 1dy5_full_validation.pdf.gz | 457 KB | Display | |
Data in XML | 1dy5_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 1dy5_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/1dy5 ftp://data.pdbj.org/pub/pdb/validation_reports/dy/1dy5 | HTTPS FTP |
-Related structure data
Related structure data | 1lsqS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13709.311 Da / Num. of mol.: 2 / Mutation: YES / Source method: isolated from a natural source / Details: ASN 67 REPLACED BY A BETA-ASPARTYL RESIDUE / Source: (natural) BOS TAURUS (cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5 #2: Chemical | #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-IPA / #5: Water | ChemComp-HOH / | Compound details | POSITION 67 IS THE DEAMIDATION SITE. AT THIS POSITION THERE IS A BETA-ASPARTYL RESIDUE (OR ...POSITION 67 IS THE DEAMIDATIO | Sequence details | POSITION 67 IS THE DEAMIDATION SITE. AT THIS POSITION THERE IS A BETA-ASPARTYL RESIDUE (OR ...POSITION 67 IS THE DEAMIDATIO | |
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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: 1.88 Å3/Da / Density % sol: 34.43 % | ||||||||||||||||||||||||
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Crystal grow | Method: liquid diffusion / pH: 5.7 Details: FREE LIQUID DIFFUSION METHOD USED. THE PROTEIN WAS CRYSTALLIZED FROM 50% ISOPROPANOL, 0.05 M AMMONIUM ACETATE, PH 5.7, CONC.=10 MG/ML | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: unknown / Details: Capasso, S., (1996) J.Mol.Biol., 257, 492. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.888 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1996 / Details: BENT MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.888 Å / Relative weight: 1 |
Reflection | Resolution: 0.87→61 Å / Num. obs: 160386 / % possible obs: 96.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 25.5 |
Reflection shell | Resolution: 0.87→0.88 Å / Redundancy: 1.35 % / Rmerge(I) obs: 0.104 / Mean I/σ(I) obs: 6.4 / % possible all: 68.8 |
Reflection | *PLUS Num. measured all: 493374 |
Reflection shell | *PLUS % possible obs: 68.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LSQ Resolution: 0.87→61 Å / Num. parameters: 22157 / Num. restraintsaints: 26709 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: NO GEOMETRIC RESTRAINTS APPLIED TO IAS RESIDUE. DUE TO POORLY DEFINED DENSITY, THE FOLLOWING ATOMS: (CE,NZ) AND (CG,CD,CE,NZ) ARE MISSING FROM RESIDUES B31 E B37, RESPECTIVELY. FOR RESIDUE ...Details: NO GEOMETRIC RESTRAINTS APPLIED TO IAS RESIDUE. DUE TO POORLY DEFINED DENSITY, THE FOLLOWING ATOMS: (CE,NZ) AND (CG,CD,CE,NZ) ARE MISSING FROM RESIDUES B31 E B37, RESPECTIVELY. FOR RESIDUE A37 ONLY A SINGLE SIDE CHAIN CONFORMATION HAS BEEN MODELED WHICH IS ALTERNATIVE TO A34 SIDE CHAIN AT MINOR OCCUPANCY. THE NUMBER OF PROTEIN ATOMS USED IN REFINEMENT (GIVEN ABOVE) INCLUDES CONTRIBUTIONS FROM THE MULTIPLE CONFORMERS AND ATOMS BELONGING TO THE IAS RESIDUES.
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 38 / Occupancy sum hydrogen: 1776.33 / Occupancy sum non hydrogen: 2287.34 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.87→61 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.1 / Rfactor Rwork: 0.1009 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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