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Open data
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Basic information
Entry | Database: PDB / ID: 5ark | ||||||
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Title | crystal structure of porcine RNase 4 in complex with dUMP | ||||||
![]() | 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 | ![]() | 111.3 KB | Display | ![]() |
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PDB format | ![]() | 86.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 21.5 KB | Display | |
Data in CIF | ![]() | 28 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ar6SC ![]() 5arjC ![]() 5arlC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 15708.801 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 29-147 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P15468, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters #2: Chemical | ChemComp-UMP / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.1 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 0.1 M SODIUM PHOSPHATE PH 6.5, 12 % PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→58.5 Å / Num. obs: 29780 / % possible obs: 98.2 % / Observed criterion σ(I): 6 / Redundancy: 4.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.28→2.34 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.2 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 5AR6 Resolution: 2.28→58.5 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.886 / SU B: 8.889 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.303 / ESU R Free: 0.257 / 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: 48.326 Å2
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Refinement step | Cycle: LAST / Resolution: 2.28→58.5 Å
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Refine LS restraints |
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