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Yorodumi- PDB-1tgt: ON THE DISORDERED ACTIVATION DOMAIN IN TRYPSINOGEN. CHEMICAL LABE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tgt | ||||||
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Title | ON THE DISORDERED ACTIVATION DOMAIN IN TRYPSINOGEN. CHEMICAL LABELLING AND LOW-TEMPERATURE CRYSTALLOGRAPHY | ||||||
Components | TRYPSINOGEN | ||||||
Keywords | HYDROLASE ZYMOGEN (SERINE PROTEINASE) | ||||||
Function / homology | Function and homology information trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.7 Å | ||||||
Authors | Walter, J. / Steigemann, W. / Singh, T.P. / Bartunik, H. / Bode, W. / Huber, R. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.B / Year: 1982 Title: On the Disordered Activation Domain in Trypsinogen. Chemical Labelling and Low-Temperature Crystallography Authors: Walter, J. / Steigemann, W. / Singh, T.P. / Bartunik, H. / Bode, W. / Huber, R. #1: Journal: Acta Crystallogr.,Sect.B / Year: 1983 Title: The Geometry of the Reactive Site and of the Peptide Groups in Trypsin. Trypsinogen and its Complexes with Inhibitors Authors: Marquart, M. / Walter, J. / Deisenhofer, J. / Bode, W. / Huber, R. #2: Journal: Acta Crystallogr.,Sect.B / Year: 1980 Title: Low-Temperature Protein Crystallography. Effect on Flexibility, Temperature Factor, Mosaic Spread, Extinction, and Diffuse Scattering in Two Examples. Bovine Trypsinogen and Fc Fragment Authors: Singh, T.P. / Bode, W. / Huber, R. #3: Journal: Acc.Chem.Res. / Year: 1978 Title: Structural Basis of the Activation and Action of Trypsin Authors: Huber, R. / Bode, W. #4: Journal: FEBS Lett. / Year: 1978 Title: Crystal Structure Analysis and Refinement of Two Variants of Trigonal Trypsinogen Authors: Bode, W. / Huber, R. #5: Journal: J.Mol.Biol. / Year: 1977 Title: Crystal Structure of Bovine Trypsinogen at 1.8 Angstroms Resolution. II. Crystallographic Refinement, Refined Crystal Structure and Comparison with Bovine Trypsin Authors: Fehlhammer, H. / Bode, W. / Huber, R. #6: Journal: J.Mol.Biol. / Year: 1976 Title: Crystal Structure of Bovine Trypsinogen at 1.8 Angstroms Resolution. I. Data Collection, Application of Patterson Search Techniques and Preliminary Structural Interpretation Authors: Bode, W. / Fehlhammer, H. / Huber, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tgt.cif.gz | 50.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tgt.ent.gz | 40.2 KB | Display | PDB format |
PDBx/mmJSON format | 1tgt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tg/1tgt ftp://data.pdbj.org/pub/pdb/validation_reports/tg/1tgt | 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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Atom site foot note | 1: SEE REMARKS 4 AND 6. |
-Components
#1: Protein | Mass: 24012.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Tissue: PANCREAS / References: UniProt: P00760 | ||||
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#2: Chemical | ChemComp-CA / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE 229 AMINO ACIDS OF TRYPSINOGE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.53 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.7 Å / Num. obs: 15890 / % possible obs: 72.4 % / Observed criterion σ(I): 2.5 / Num. measured all: 34340 / Rmerge(I) obs: 0.062 |
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-Processing
Refinement | Resolution: 1.7→6.5 Å / Rfactor Rwork: 0.187 Details: THERE ARE FOUR *FLEXIBLE* SEGMENTS FOR WHICH THERE IS NO SIGNIFICANT ELECTRON DENSITY IN THE MAP. THESE ARE 1. THREE CLOSELY INTERDIGITATING CHAIN SEGMENTS FORMING THE ACTIVATION DOMAIN GLY ...Details: THERE ARE FOUR *FLEXIBLE* SEGMENTS FOR WHICH THERE IS NO SIGNIFICANT ELECTRON DENSITY IN THE MAP. THESE ARE 1. THREE CLOSELY INTERDIGITATING CHAIN SEGMENTS FORMING THE ACTIVATION DOMAIN GLY 142 - PRO 152 GLY 184A - GLY 193 GLY 216 - ASN 223 2. THE N-TERMINUS FROM VAL 10 THROUGH GLY 18 (THIS DATA ENTRY CONTAINS NO COORDINATES FOR VAL 10 THROUGH LYS 15) | ||||||||||||
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Refinement step | Cycle: LAST / Resolution: 1.7→6.5 Å
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Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 6.5 Å / Num. reflection obs: 15890 / Rfactor obs: 0.187 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS Biso mean: 11.6 Å2 | ||||||||||||
Refine LS restraints | *PLUS Type: o_bond_d / Dev ideal: 0.19 | ||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.73 Å / Lowest resolution: 6.5 Å |