+Open data
-Basic information
Entry | Database: PDB / ID: 2blw | ||||||
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Title | Trypsin after a high dose X-ray "Burn" | ||||||
Components | TRYPSIN | ||||||
Keywords | HYDROLASE / RADIATION DAMAGE / SYNCHROTRON / PHASING / RIP / CALCIUM-BINDING / DIGESTION / PANCREAS / PROTEASE / SERINE PROTEASE | ||||||
Function / homology | Function and homology information trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | BOS TAURUS (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.2 Å | ||||||
Authors | Nanao, M.H. / Ravelli, R.B. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / 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 DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2blw.cif.gz | 113.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2blw.ent.gz | 94 KB | Display | PDB format |
PDBx/mmJSON format | 2blw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/2blw ftp://data.pdbj.org/pub/pdb/validation_reports/bl/2blw | HTTPS FTP |
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-Related structure data
Related structure data | 2bloC 2blpC 2blqC 2blrC 2bluC 2blvC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: PANCREAS / References: UniProt: P00760, trypsin |
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-Non-polymers , 5 types, 321 molecules
#2: Chemical | ChemComp-CA / | ||||
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#3: Chemical | ChemComp-BEN / | ||||
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-GOL / | #6: 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: 1.77 Å3/Da / Density % sol: 30.04 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9392 |
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: 1.2→50 Å / Num. obs: 122363 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.15 |
Reflection shell | Resolution: 1.2→1.3 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 5.75 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.2→10 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.666 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.03 / 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 VAL 53, LYS 109, ASN 115, ...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 VAL 53, LYS 109, ASN 115, SER 116, LYS 145, LYS 169, SER 178, GLU 186, GLN 240
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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: 6.43 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→10 Å
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Refine LS restraints |
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