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Yorodumi- PDB-3dic: Crystal structure of bovine pancreatic ribonuclease A variant (V108A) -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dic | ||||||
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Title | Crystal structure of bovine pancreatic ribonuclease A variant (V108A) | ||||||
Components | Ribonuclease pancreatic | ||||||
Keywords | HYDROLASE / ribonuclease / RNase A / Bovine pancreas / Endonuclease / Glycation / Glycoprotein / Nuclease / Secreted | ||||||
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: 1.6 Å | ||||||
Authors | Kurpiewska, K. / Font, J. / Ribo, M. / Vilanova, M. / Lewinski, K. | ||||||
Citation | Journal: Proteins / Year: 2009 Title: X-ray crystallographic studies of RNase A variants engineered at the most destabilizing positions of the main hydrophobic core: further insight into protein stability Authors: Kurpiewska, K. / Font, J. / Ribo, M. / Vilanova, M. / Lewinski, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dic.cif.gz | 42.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dic.ent.gz | 28.7 KB | Display | PDB format |
PDBx/mmJSON format | 3dic.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dic_validation.pdf.gz | 434.6 KB | Display | wwPDB validaton report |
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Full document | 3dic_full_validation.pdf.gz | 435.4 KB | Display | |
Data in XML | 3dic_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 3dic_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/3dic ftp://data.pdbj.org/pub/pdb/validation_reports/di/3dic | HTTPS FTP |
-Related structure data
Related structure data | 3dh5C 3dh6C 3di7C 3di8C 3di9C 3dibC 1fs3S C: citing same article (ref.) 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: 13680.272 Da / Num. of mol.: 1 / Mutation: V108A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: RNASE1, RNS1 / Plasmid: pBXR / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.27 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: ammonium sulfate, sodium chloride, sodium acetate, pH 6.0, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 273 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SEALED TUBE / Type: ENRAF-NONIUS FR590 / Wavelength: 0.7107 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: Nonius Kappa CCD / Detector: CCD / Date: Apr 27, 2005 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.7107 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.47→99 Å / Num. obs: 25612 / % possible obs: 99.1 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.135 / Χ2: 8.598 / Net I/σ(I): 9.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FS3 Resolution: 1.6→10 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 112532.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.2948 Å2 / ksol: 0.50935 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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