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Yorodumi- PDB-1trm: THE THREE-DIMENSIONAL STRUCTURE OF ASN102 MUTANT OF TRYPSIN. ROLE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1trm | ||||||
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Title | THE THREE-DIMENSIONAL STRUCTURE OF ASN102 MUTANT OF TRYPSIN. ROLE OF ASP102 IN SERINE PROTEASE CATALYSIS | ||||||
Components | TRYPSIN | ||||||
Keywords | HYDROLASE (SERINE PROTEINASE) | ||||||
Function / homology | Function and homology information Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / Neutrophil degranulation / collagen catabolic process / trypsin / digestion / response to nutrient / serine-type endopeptidase activity / calcium ion binding ...Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / Neutrophil degranulation / collagen catabolic process / trypsin / digestion / response to nutrient / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Rattus rattus (black rat) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Sprang, S. / Standing, T. / Fletterick, R.J. | ||||||
Citation | Journal: Science / Year: 1987 Title: The three-dimensional structure of Asn102 mutant of trypsin: role of Asp102 in serine protease catalysis. Authors: Sprang, S. / Standing, T. / Fletterick, R.J. / Stroud, R.M. / Finer-Moore, J. / Xuong, N.H. / Hamlin, R. / Rutter, W.J. / Craik, C.S. #1: Journal: Science / Year: 1987 Title: The Catalytic Role of the Active Site Aspartic Acid in Serine Proteases Authors: Craik, C.S. / Roczniak, S. / Largman, C. / Rutter, W.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1trm.cif.gz | 100.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1trm.ent.gz | 80.1 KB | Display | PDB format |
PDBx/mmJSON format | 1trm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1trm_validation.pdf.gz | 396.4 KB | Display | wwPDB validaton report |
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Full document | 1trm_full_validation.pdf.gz | 437 KB | Display | |
Data in XML | 1trm_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 1trm_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/1trm ftp://data.pdbj.org/pub/pdb/validation_reports/tr/1trm | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: SEE REMARK 5. |
-Components
#1: Protein | Mass: 23813.854 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus rattus (black rat) / References: UniProt: P00763, trypsin #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | THE CATALYTIC SITE, DIFFERS FROM THE CATALYTIC SITE OF NATIVE TRYPSIN BY REPLACEMENT OF ASP 102 ...THE CATALYTIC SITE, DIFFERS FROM THE CATALYTIC SITE OF NATIVE TRYPSIN BY REPLACEMEN | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.45 % | ||||||||||||
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Crystal grow | *PLUS pH: 6 / Method: vapor diffusion | ||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.3 Å / Num. obs: 22000 / Num. measured all: 90000 / Rmerge F obs: 0.05 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.3→6 Å / Rfactor obs: 0.16 Details: THE A AND B CONFORMATIONS OF THE RESIDUE HIS 57 IN BOTH CHAINS WERE OBSERVED IN DIFFERENCE MAPS AFTER REFINEMENT WITH THIS SIDE CHAIN OMITTED FROM THE MODEL. THE POSSIBILITY THAT ONE OF THE ...Details: THE A AND B CONFORMATIONS OF THE RESIDUE HIS 57 IN BOTH CHAINS WERE OBSERVED IN DIFFERENCE MAPS AFTER REFINEMENT WITH THIS SIDE CHAIN OMITTED FROM THE MODEL. THE POSSIBILITY THAT ONE OF THE POSITIONS WOULD CORRESPOND TO AN ORDERED WATER MOLECULE WAS TESTED AND FOUND TO BE INCORRECT. THE RELATIVE OCCUPANCY OF THE TWO CONFORMATIONS WAS ESTIMATED BY COMPARING THE ELECTRON DENSITY AT POSITIONS WHERE THE TWO SIDE CHAINS DO NOT OVERLAP. THE OCCUPANCY OF THE TWO POSITIONS WAS NOT REFINED. THE B CONFORMATION CORRESPONDS TO THAT FOUND IN WILD TYPE TRYPSIN. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→6 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 6 Å / Rfactor obs: 0.16 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |