+Open data
-Basic information
Entry | Database: PDB / ID: 5arj | ||||||
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Title | crystal structure of porcine RNase 4 D80A mutant | ||||||
Components | RIBONUCLEASE 4 | ||||||
Keywords | HYDROLASE / RNA DEGRADATION | ||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA nuclease activity / antibacterial humoral response / endonuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / extracellular space Similarity search - Function | ||||||
Biological species | SUS SCROFA (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Liang, S. / Acharya, K.R. | ||||||
Citation | Journal: FEBS J. / Year: 2016 Title: Structural Basis of Substrate Specificity in Porcine Rnase 4. Authors: Liang, S. / Acharya, K.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5arj.cif.gz | 105.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5arj.ent.gz | 82.7 KB | Display | PDB format |
PDBx/mmJSON format | 5arj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5arj_validation.pdf.gz | 451.6 KB | Display | wwPDB validaton report |
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Full document | 5arj_full_validation.pdf.gz | 453.6 KB | Display | |
Data in XML | 5arj_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 5arj_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/5arj ftp://data.pdbj.org/pub/pdb/validation_reports/ar/5arj | HTTPS FTP |
-Related structure data
Related structure data | 5ar6SC 5arkC 5arlC 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 15664.789 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SUS SCROFA (pig) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P15468, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters Sequence details | THE FIRST ALA IS FROM THE N-TERMINAL TAG. DUE TO THE LACK OF SIDE CHAIN ELECTRON DENSITY, THE ...THE FIRST ALA IS FROM THE N-TERMINAL TAG. DUE TO THE LACK OF SIDE CHAIN ELECTRON DENSITY, THE RESIDUE IS SHOWN AS ALA. THE FIRST TWO ALA ARE FROM THE N-TERMINAL TAG. DUE TO THE LACK OF SIDE CHAIN ELECTRON DENSITY, THE RESIDUES ARE SHOWN AS ALA. | |
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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: 2.03 Å3/Da / Density % sol: 39.54 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.1 M SODIUM CACODYLATE PH 6.5, 1.0 M SODIUM CITRATE TRIBASIC DIHYDRATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→29.39 Å / Num. obs: 7962 / % possible obs: 73.5 % / Observed criterion σ(I): 6 / Redundancy: 1.6 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.9→3.08 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 2 / % possible all: 75.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5AR6. Resolution: 2.9→67.43 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.858 / SU B: 27.855 / SU ML: 0.49 / Cross valid method: THROUGHOUT / ESU R Free: 0.654 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.308 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→67.43 Å
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Refine LS restraints |
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