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Yorodumi- PDB-4ao1: High resolution crystal structure of bovine pancreatic ribonuclea... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ao1 | ||||||
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Title | High resolution crystal structure of bovine pancreatic ribonuclease crystallized using ionic liquid | ||||||
Components | RIBONUCLEASE PANCREATIC | ||||||
Keywords | HYDROLASE | ||||||
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: 1.58 Å | ||||||
Authors | Mukhopadhyay, A. / Carvalho, A.L. / Kowacz, M. / Romao, M.J. | ||||||
Citation | Journal: Cryst.Eng.Comm. / Year: 2012 Title: Hofmeister Effects of Ionic Liquids in Protein Crystallization: Direct and Water-Mediated Interactions Authors: Kowacz, M. / Mukhopadhyay, A. / Carvalho, A.L. / Esperanca, J.M.S.S. / Romao, M.J. / Rebelo, L.P.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ao1.cif.gz | 45.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ao1.ent.gz | 32.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ao1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ao1_validation.pdf.gz | 442.5 KB | Display | wwPDB validaton report |
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Full document | 4ao1_full_validation.pdf.gz | 443.6 KB | Display | |
Data in XML | 4ao1_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 4ao1_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/4ao1 ftp://data.pdbj.org/pub/pdb/validation_reports/ao/4ao1 | HTTPS FTP |
-Related structure data
Related structure data | 4agaC 3i67S S: Starting model for refinement C: citing same article (ref.) |
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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: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / References: UniProt: P61823, EC: 3.1.27.5 | ||||
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#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 5 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.41 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 4.5 Details: RIBONUCLEASE A FROM BOVINE PANCREAS (SIGMA) HAS BEEN DISSOLVED IN 50 MM SODIUM ACETATE BUFFER (PH 4.57) AND CRYSTALLIZED BY THE SITTING DROP DIFFUSION METHOD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.99188 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99188 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→31.81 Å / Num. obs: 18627 / % possible obs: 93.7 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 26.7 |
Reflection shell | Resolution: 1.58→1.67 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 19.2 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3I67 Resolution: 1.58→55.43 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.921 / SU B: 1.11 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.794 Å2
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Refinement step | Cycle: LAST / Resolution: 1.58→55.43 Å
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Refine LS restraints |
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