+Open data
-Basic information
Entry | Database: PDB / ID: 1lsq | ||||||
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Title | RIBONUCLEASE A WITH ASN 67 REPLACED BY A BETA-ASPARTYL RESIDUE | ||||||
Components | RIBONUCLEASE APancreatic ribonuclease family | ||||||
Keywords | HYDROLASE / PHOSPHORIC DIESTER | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Esposito, L. / Sica, F. / Vitagliano, L. / Zagari, A. / Mazzarella, L. | ||||||
Citation | 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. #1: Journal: J.Biol.Chem. / Year: 1993 Title: Selective Deamidation of Ribonuclease A Authors: Di Donato, A. / Ciardiello, M.A. / De Nigris, M. / Piccoli, R. / Mazzarella, L. / D'Alessio, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lsq.cif.gz | 57.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lsq.ent.gz | 45.4 KB | Display | PDB format |
PDBx/mmJSON format | 1lsq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/1lsq ftp://data.pdbj.org/pub/pdb/validation_reports/ls/1lsq | HTTPS FTP |
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-Related structure data
Related structure data | 5rsaS 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 / Source method: isolated from a natural source / Details: ASN 67 IS REPLACED BY A BETA-ASPARTYL RESIDUE / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 38 % | ||||||||||||||||||||||||
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Crystal | *PLUS | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 5.7 / Method: unknown | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: BRUKER NONIUS CAD4 / Detector: DIFFRACTOMETER / Date: Apr 1, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 17221 / % possible obs: 99.4 % / Redundancy: 1.4 % / Rmerge(I) obs: 0.051 |
Reflection | *PLUS Highest resolution: 1.9 Å / Num. measured all: 23907 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5RSA Resolution: 1.9→20 Å / σ(F): 1 Details: THE SULFATE IONS IN THE ACTIVE SITES HAVE LOW DENSITY AND HIGH TEMPERATURE FACTORS. OCCUPANCY FACTORS HAVE NOT BEEN REFINED.
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Displacement parameters | Biso mean: 13.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.168 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |