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Yorodumi- PDB-1a0j: CRYSTAL STRUCTURE OF A NON-PSYCHROPHILIC TRYPSIN FROM A COLD-ADAP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a0j | ||||||
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Title | CRYSTAL STRUCTURE OF A NON-PSYCHROPHILIC TRYPSIN FROM A COLD-ADAPTED FISH SPECIES. | ||||||
Components | TRYPSIN | ||||||
Keywords | SERINE PROTEASE / SERINE PROTEINASE / TRYPSIN / HYDROLASE | ||||||
Function / homology | Function and homology information trypsin / digestion / serine-type endopeptidase activity / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Salmo salar (Atlantic salmon) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Schroeder, H.-K. / Willassen, N.P. / Smalaas, A.O. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Structure of a non-psychrophilic trypsin from a cold-adapted fish species. Authors: Schroder, H.K. / Willassen, N.P. / Smalas, A.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a0j.cif.gz | 183.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a0j.ent.gz | 148.4 KB | Display | PDB format |
PDBx/mmJSON format | 1a0j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/1a0j ftp://data.pdbj.org/pub/pdb/validation_reports/a0/1a0j | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 23803.662 Da / Num. of mol.: 4 / Source method: isolated from a natural source Details: BENZAMIDINE INHIBITOR IN THE ACTIVE SITE. THE AMINO ACID NUMBERING SCHEME USED IS ADOPTED FROM CHYMOTRYPSINOGEN. Source: (natural) Salmo salar (Atlantic salmon) / Organ: PANCREAS / References: UniProt: P35033, trypsin #2: Chemical | ChemComp-CA / | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-BEN / #5: Water | ChemComp-HOH / | Sequence details | THE AMINO ACID NUMBERING SCHEME USED IS ADOPTED FROM CHYMOTRYPS | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % | |||||||||||||||||||||||||
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Crystal grow | pH: 4.6 / Details: pH 4.6 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 310 K / Method: vapor diffusionDetails: drop contained 1:1 mixture of protein and reservoir solution | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.873 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→28 Å / Num. obs: 76357 / % possible obs: 81.2 % / Observed criterion σ(I): 1 / Redundancy: 5.9 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 3.6 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 2 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 2.9 / % possible all: 52.3 |
Reflection | *PLUS Num. measured all: 451079 |
Reflection shell | *PLUS % possible obs: 52.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3PTB BOVINE TRYPSIN, WITH CORRECT AMINO ACID SEQUENCE SUPERIMPOSED ONTO ANIONIC SALMON TRYPSIN 2TBS. Resolution: 1.7→8 Å / Cross valid method: THROUGHOUT / σ(F): 3 Details: NCS RESTRAINTS WERE INCLUDED IN THE FIRST REFINEMENT ROUNDS, THEN LEFT OUT. THE ELECTRON DENSITY INDICATES A CALCIUM ION FOR ONLY ONE OF THE FOUR MOLECULES (MOL A). THE ELECTRON DENSITY ...Details: NCS RESTRAINTS WERE INCLUDED IN THE FIRST REFINEMENT ROUNDS, THEN LEFT OUT. THE ELECTRON DENSITY INDICATES A CALCIUM ION FOR ONLY ONE OF THE FOUR MOLECULES (MOL A). THE ELECTRON DENSITY INDICATES A CALCIUM ION FOR ONLY ONE OF THE FOUR MOLECULES (MOL A).
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Displacement parameters | Biso mean: 22.93 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error free: 0.18 Å / Luzzati sigma a free: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.76 Å / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.2347 |