+Open data
-Basic information
Entry | Database: PDB / ID: 1hj8 | |||||||||
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Title | 1.00 AA Trypsin from Atlantic Salmon | |||||||||
Components | TRYPSIN I | |||||||||
Keywords | HYDROLASE / RADIATION DAMAGE / DISULPHIDE BOND BREAKAGE / SALMON / TRYPSIN / ATOMIC RESOLUTION | |||||||||
Function / homology | Function and homology information trypsin / digestion / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | SALMO SALAR (Atlantic salmon) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å | |||||||||
Authors | Leiros, H.-K.S. / Mcsweeney, S.M. / Smalas, A.O. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Atomic Resolution Structure of Trypsin Provide Insight Into Structural Radiation Damage Authors: Leiros, H.-K.S. / Mcsweeney, S.M. / Smalas, A.O. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "B" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "B" 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 | 1hj8.cif.gz | 172.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hj8.ent.gz | 133.1 KB | Display | PDB format |
PDBx/mmJSON format | 1hj8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hj/1hj8 ftp://data.pdbj.org/pub/pdb/validation_reports/hj/1hj8 | HTTPS FTP |
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-Related structure data
Related structure data | 1hj9C 1bitS S: Starting model for refinement 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
#1: Protein | Mass: 23835.725 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-242 / Source method: isolated from a natural source / Source: (natural) SALMO SALAR (Atlantic salmon) / References: UniProt: P35031, trypsin | ||||||
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#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-CA / | #5: 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: 1.95 Å3/Da / Density % sol: 36.91 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.8 / Details: pH 5.80 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 310 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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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: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1→15 Å / Num. obs: 76713 / % possible obs: 76.5 % / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 1→1.05 Å / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 3.2 / % possible all: 53.4 |
Reflection | *PLUS Lowest resolution: 15 Å / Num. measured all: 174662 / Rmerge(I) obs: 0.049 |
Reflection shell | *PLUS % possible obs: 53.4 % / Rmerge(I) obs: 0.232 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BIT Resolution: 1→8 Å / Num. parameters: 18565 / Num. restraintsaints: 24964 / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 39 / Occupancy sum hydrogen: 1503.5 / Occupancy sum non hydrogen: 1852.8 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→8 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.118 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |