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Open data
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Basic information
Entry | Database: PDB / ID: 2blz | ||||||
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Title | RNAse after a high dose X-ray "burn" | ||||||
![]() | RIBONUCLEASE PANCREATIC | ||||||
![]() | HYDROLASE / RADIATION DAMAGE / SYNCHROTRON / PHASING / RIP / ENDONUCLEASE / GLYCOPROTEIN / NUCLEASE | ||||||
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 | ![]() ![]() | ||||||
![]() | Nanao, M.H. / Ravelli, R.B. | ||||||
![]() | ![]() Title: Improving Radiation-Damage Substructures for Rip. Authors: Nanao, M.H. / Sheldrick, G.M. / Ravelli, R.B. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.3 KB | Display | ![]() |
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PDB format | ![]() | 52.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 416.2 KB | Display | ![]() |
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Full document | ![]() | 417 KB | Display | |
Data in XML | ![]() | 8.6 KB | Display | |
Data in CIF | ![]() | 11.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bloC ![]() 2blpC ![]() 2blqC ![]() 2blrC ![]() 2bluC ![]() 2blvC ![]() 2blwC ![]() 2blxC ![]() 2blyC ![]() 2bn1C ![]() 2bn3C 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
Compound details | FUNCTION: CATALYZES THE CLEAVAGE OF RNA ON THE 3' SIDE OF PYRIMIDINE NUCLEOTIDES. ACTS ON SINGLE ...FUNCTION: CATALYZES THE CLEAVAGE OF RNA ON THE 3' SIDE OF PYRIMIDINE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.56 % |
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Crystal grow | Details: 30 % PEG 5000 MME, 1 M SODIUM CHLORIDE,50 MM PH 4.5 SODIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 18, 2004 / Details: BENT MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9392 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 24403 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.15 |
Reflection shell | Resolution: 1.5→1.59 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.67 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: OTHER / Resolution: 1.4→45 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.671 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SIDECHAIN OCCUPANCIES HAVE BEEN REDUCED BECAUSE OF STRONG NEGATIVE PEAKS IN DIFFERENCE FOURIER MAPS IN RESIDUES LYS 1, LYS 31, LYS 37, ASP ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SIDECHAIN OCCUPANCIES HAVE BEEN REDUCED BECAUSE OF STRONG NEGATIVE PEAKS IN DIFFERENCE FOURIER MAPS IN RESIDUES LYS 1, LYS 31, LYS 37, ASP 38, ARG 39, LYS 91, LYS 104
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.71 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→45 Å
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Refine LS restraints |
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