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Yorodumi- PDB-1trn: CRYSTAL STRUCTURE OF HUMAN TRYPSIN 1: UNEXPECTED PHOSPHORYLATION ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1trn | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN TRYPSIN 1: UNEXPECTED PHOSPHORYLATION OF TYROSINE 151 | ||||||
Components | TRYPSIN | ||||||
Keywords | HYDROLASE (SERINE PROTEINASE) / HUMAN TRYPSIN / DFP INHIBITED | ||||||
Function / homology | Function and homology information Uptake of dietary cobalamins into enterocytes / Activation of Matrix Metalloproteinases / extracellular matrix disassembly / trypsin / digestion / collagen-containing extracellular matrix / blood microparticle / serine-type endopeptidase activity / proteolysis / extracellular space ...Uptake of dietary cobalamins into enterocytes / Activation of Matrix Metalloproteinases / extracellular matrix disassembly / trypsin / digestion / collagen-containing extracellular matrix / blood microparticle / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
Authors | Gaboriaud, C. / Fontecilla-Camps, J.C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1996 Title: Crystal structure of human trypsin 1: unexpected phosphorylation of Tyr151. Authors: Gaboriaud, C. / Serre, L. / Guy-Crotte, O. / Forest, E. / Fontecilla-Camps, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1trn.cif.gz | 98 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1trn.ent.gz | 80.3 KB | Display | PDB format |
PDBx/mmJSON format | 1trn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/1trn ftp://data.pdbj.org/pub/pdb/validation_reports/tr/1trn | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.683235, -0.730181, 0.005026), Vector: Details | MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 B 16 .. B 302 A 16 .. A 302 0.311 | |
-Components
#1: Protein | Mass: 24217.180 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P07477, trypsin #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.96 % | |||||||||||||||||||||||||
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Crystal | *PLUS Density % sol: 50 % | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9 |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1992 |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Num. obs: 22989 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.044 |
Reflection | *PLUS Highest resolution: 2.18 Å / Lowest resolution: 10 Å / Num. measured all: 63716 / Rmerge(I) obs: 0.044 / Biso Wilson estimate: 30.6 Å2 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.23 Å / % possible obs: 91.7 % |
-Processing
Software |
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Refinement | Resolution: 2.2→10 Å / σ(F): 0
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Displacement parameters | Biso mean: 32.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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