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Open data
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Basic information
Entry | Database: PDB / ID: 5ar6 | ||||||
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Title | crystal structure of porcine RNase 4 | ||||||
![]() | RIBONUCLEASE 4 | ||||||
![]() | HYDROLASE / RIBONUCLEASE 4 / RNA DEGRADATION | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liang, S. / Acharya, K.R. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.6 KB | Display | ![]() |
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PDB format | ![]() | 51.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.1 KB | Display | ![]() |
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Full document | ![]() | 424.5 KB | Display | |
Data in XML | ![]() | 8.4 KB | Display | |
Data in CIF | ![]() | 11.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5arjC ![]() 5arkC ![]() 5arlC ![]() 1rnfS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14131.139 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P15468, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.16 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 0.1 M MORPHEUS BUFFER SYSTEM 3 PH 8.5, 0.12 M MONOSACCHARIDES, 30 % (V/V) EDO_P8K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Dec 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→43.07 Å / Num. obs: 32743 / % possible obs: 99.9 % / Observed criterion σ(I): 6 / Redundancy: 6.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.25→1.27 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4.4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1RNF Resolution: 1.25→43.07 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.069 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.037 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.532 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→43.07 Å
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Refine LS restraints |
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