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- PDB-1a0j: CRYSTAL STRUCTURE OF A NON-PSYCHROPHILIC TRYPSIN FROM A COLD-ADAP... -
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Open data
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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. | ||||||
![]() | TRYPSIN | ||||||
![]() | SERINE PROTEASE / SERINE PROTEINASE / TRYPSIN / HYDROLASE | ||||||
Function / homology | ![]() trypsin / digestion / serine-type endopeptidase activity / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schroeder, H.-K. / Willassen, N.P. / Smalaas, A.O. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 183.6 KB | Display | ![]() |
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PDB format | ![]() | 148.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 478.3 KB | Display | ![]() |
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Full document | ![]() | 492 KB | Display | |
Data in XML | ![]() | 38.1 KB | Display | |
Data in CIF | ![]() | 53 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() ![]() #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: ![]() |
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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: ![]() ![]() ![]() |
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 % |
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Processing
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Refinement | Method to determine structure: ![]() 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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.2347 |