+Open data
-Basic information
Entry | Database: PDB / ID: 2blp | ||||||
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Title | RNase before unattenuated X-RAY burn | ||||||
Components | RIBONUCLEASE PANCREATIC PRECURSOR | ||||||
Keywords | HYDROLASE / RADIATION DAMAGE / SYNCHROTRON / PHASING / RIP | ||||||
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 / SYNCHROTRON / OTHER / Resolution: 1.4 Å | ||||||
Authors | Nanao, M.H. / Ravelli, R.B. | ||||||
Citation | Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2005 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2blp.cif.gz | 64.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2blp.ent.gz | 52.8 KB | Display | PDB format |
PDBx/mmJSON format | 2blp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2blp_validation.pdf.gz | 418.8 KB | Display | wwPDB validaton report |
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Full document | 2blp_full_validation.pdf.gz | 419.6 KB | Display | |
Data in XML | 2blp_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 2blp_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/2blp ftp://data.pdbj.org/pub/pdb/validation_reports/bl/2blp | HTTPS FTP |
-Related structure data
Related structure data | 2bloC 2blqC 2blrC 2bluC 2blvC 2blwC 2blxC 2blyC 2blzC 2bn1C 2bn3C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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) BOS TAURUS (cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5 |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
Compound details | ENDONUCLEASE THAT CATALYZES THE CLEAVAGE OF RNA ON THE 3' SIDE OF PYRIMIDINE NUCLEOTIDES. ACTS ON ...ENDONUCLEA |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.5 % |
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Crystal grow | pH: 5.5 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: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939255 |
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: 0.939255 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 55873 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 10.93 |
Reflection shell | Resolution: 1.4→1.49 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.25 / % possible all: 90.3 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.4→45 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.414 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.05 / 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: 11.12 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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