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- PDB-3di7: Crystal structure of bovine pancreatic ribonuclease A variant (V54A) -
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Open data
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Basic information
Entry | Database: PDB / ID: 3di7 | ||||||
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Title | Crystal structure of bovine pancreatic ribonuclease A variant (V54A) | ||||||
![]() | Ribonuclease pancreatic | ||||||
![]() | HYDROLASE / ribonuclease / RNase A / Bovine pancreas / Endonuclease / Glycation / Glycoprotein / Nuclease / Secreted | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kurpiewska, K. / Font, J. / Ribo, M. / Vilanova, M. / Lewinski, K. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 43.3 KB | Display | ![]() |
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PDB format | ![]() | 29 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 408.1 KB | Display | ![]() |
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Full document | ![]() | 409.3 KB | Display | |
Data in XML | ![]() | 5 KB | Display | |
Data in CIF | ![]() | 7.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3dh5C ![]() 3dh6C ![]() 3di8C ![]() 3di9C ![]() 3dibC ![]() 3dicC ![]() 1fs3S 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13680.273 Da / Num. of mol.: 1 / Mutation: V54A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.38 % |
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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: Mar 17, 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: 1.4→10 Å / Num. obs: 23442 / % possible obs: 90.8 % / Rmerge(I) obs: 0.111 / Χ2: 1.927 / Net I/σ(I): 9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1FS3 Resolution: 1.6→6 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 101687 / 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: 51.045 Å2 / ksol: 0.398 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 61.32 Å2 / Biso mean: 16.617 Å2 / Biso min: 1.71 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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