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- PDB-3jw1: Crystal Structure of Bovine Pancreatic Ribonuclease Complexed wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3jw1 | ||||||
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Title | Crystal Structure of Bovine Pancreatic Ribonuclease Complexed with Uridine-5'-monophosphate at 1.60 A Resolution | ||||||
![]() | Ribonuclease pancreatic | ||||||
![]() | HYDROLASE / Ribonuclease A / Uridine-5'-monophosphate / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for High-Throughput Structural Biology / CHTSB / 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 | ![]() ![]() | ||||||
![]() | Larson, S.B. / Day, J.S. / Nguyen, C. / Cudney, R. / Mcpherson, A. / Center for High-Throughput Structural Biology (CHTSB) | ||||||
![]() | ![]() Title: Structure of bovine pancreatic ribonuclease complexed with uridine 5'-monophosphate at 1.60 A resolution. Authors: Larson, S.B. / Day, J.S. / Nguyen, C. / Cudney, R. / McPherson, A. #1: ![]() Title: Progress in the Development of an Alternative Approach to Macromolecular Crystallization Authors: Larson, S.B. / Day, J.S. / Nguyen, C. / Cudney, R. / Mcpherson, A. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2007 Title: A novel strategy for the crystallization of proteins: X-ray diffraction validation. Authors: Larson, S.B. / Day, J.S. / Cudney, R. / McPherson, A. #3: Journal: J.Struct.Biol. / Year: 2006 Title: Searching for silver bullets: an alternative strategy for crystallizing macromolecules. Authors: McPherson, A. / Cudney, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108 KB | Display | ![]() |
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PDB format | ![]() | 85.6 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 | ![]() | 15.4 KB | Display | |
Data in CIF | ![]() | 21.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1u1bS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.04 % |
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Crystal grow | Temperature: 298 K / pH: 7 Details: 0.1 M HEPES BUFFER; Reservoir of 25% PEG3350 in water; droplets were 5-10 mM in basic fuchsin, tobramycin, uridine-5'-monophosphate and 1 mM in ribonuclease A, pH 7.0, VAPOR DIFFUSION, ...Details: 0.1 M HEPES BUFFER; Reservoir of 25% PEG3350 in water; droplets were 5-10 mM in basic fuchsin, tobramycin, uridine-5'-monophosphate and 1 mM in ribonuclease A, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 29, 2007 / Details: OSMIC MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→29.54 Å / Num. obs: 25900 / % possible obs: 91.2 % / Redundancy: 2.61 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.027 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 2.15 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.4 / % possible all: 64.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1U1B Resolution: 1.6→29.54 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 7.709 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic with TLS / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.133 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.71 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→29.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.64 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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