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Yorodumi- PDB-8tln: STRUCTURAL COMPARISON SUGGESTS THAT THERMOLYSIN AND RELATED NEUTR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8tln | |||||||||
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Title | STRUCTURAL COMPARISON SUGGESTS THAT THERMOLYSIN AND RELATED NEUTRAL PROTEASES UNDERGO HINGE-BENDING MOTION DURING CATALYSIS | |||||||||
Components | THERMOLYSIN | |||||||||
Keywords | HYDROLASE(METALLOPROTEINASE) | |||||||||
Function / homology | Function and homology information thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Bacillus thermoproteolyticus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.6 Å | |||||||||
Authors | Tronrud, D. / Matthews, B.W. | |||||||||
Citation | Journal: Biochemistry / Year: 1992 Title: Structural comparison suggests that thermolysin and related neutral proteases undergo hinge-bending motion during catalysis. Authors: Holland, D.R. / Tronrud, D.E. / Pley, H.W. / Flaherty, K.M. / Stark, W. / Jansonius, J.N. / McKay, D.B. / Matthews, B.W. #1: Journal: J.Mol.Biol. / Year: 1982 Title: Structure of Thermolysin Refined at 1.6 Angstroms Resolution Authors: Holmes, M.A. / Matthews, B.W. #2: Journal: Biochemistry / Year: 1982 Title: Structure of a Mercaptan-Thermolysin Complex Illustrates Mode of Inhibition of Zinc Proteases by Substrate-Analogue Mercaptans Authors: Monzingo, A.F. / Matthews, B.W. #3: Journal: Biochemistry / Year: 1981 Title: Binding of Hydroxamic Acid Inhibitors to Crystalline Thermolysin Suggests a Pentacoordinate Zinc Intermediate in Catalysis Authors: Holmes, M.A. / Matthews, B.W. #4: Journal: J.Biol.Chem. / Year: 1979 Title: Binding of the Biproduct Analog L-Benzylsuccinic Acid to Thermolysin Determined by X-Ray Crystallography Authors: Bolognesi, M.C. / Matthews, B.W. #5: Journal: J.Biol.Chem. / Year: 1977 Title: Comparison of the Structures of Carboxypeptidase a and Thermolysin Authors: Kester, W.R. / Matthews, B.W. #6: Journal: J.Mol.Biol. / Year: 1977 Title: A Crystallographic Study of the Complex of Phosphoramidon with Thermolysin. A Model for the Presumed Catalytic Transition State and for the Binding of Extended Substrates Authors: Weaver, L.H. / Kester, W.R. / Matthews, B.W. #7: Journal: Biochemistry / Year: 1977 Title: Crystallographic Study of the Binding of Dipeptide Inhibitors to Thermolysin. Implications for the Mechanism of Catalysis Authors: Kester, W.R. / Matthews, B.W. #8: Journal: Biochemistry / Year: 1976 Title: Role of Calcium in the Thermal Stability of Thermolysin Authors: Dahlquist, F.W. / Long, J.W. / Bigbee, W.L. #9: Journal: Proc.Natl.Acad.Sci.USA / Year: 1975 Title: Evidence of Homologous Relationship between Thermolysin and Neutral Protease a of Bacillus Subtilis Authors: Levy, P.L. / Pangburn, M.K. / Burstein, Y. / Ericsson, L.H. / Neurath, H. / Walsh, K.A. #10: Journal: J.Biol.Chem. / Year: 1974 Title: The Conformation of Thermolysin Authors: Matthews, B.W. / Weaver, L.H. / Kester, W.R. #11: Journal: Biochemistry / Year: 1974 Title: Binding of Lanthanide Ions to Thermolysin Authors: Matthews, B.W. / Weaver, L.H. #12: Journal: J.Mol.Biol. / Year: 1972 Title: The Structure of Thermolysin,an Electron Density Map at 2.3 Angstroms Resolution Authors: Colman, P.M. / Jansonius, J.N. / Matthews, B.W. #13: Journal: Nature New Biol. / Year: 1972 Title: Amino-Acid Sequence of Thermolysin Authors: Titani, K. / Hermodson, M.A. / Ericsson, L.H. / Walsh, K.A. / Neurath, H. #14: Journal: Nature New Biol. / Year: 1972 Title: Three Dimensional Structure of Thermolysin Authors: Matthews, B.W. / Jansonius, J.N. / Colman, P.M. / Schoenborn, B.P. / Duporque, D. #15: Journal: Nature New Biol. / Year: 1972 Title: Structure of Thermolysin Authors: Matthews, B.W. / Colman, P.M. / Jansonius, J.N. / Titani, K. / Walsh, K.A. / Neurath, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tln.cif.gz | 80.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tln.ent.gz | 59.9 KB | Display | PDB format |
PDBx/mmJSON format | 8tln.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/8tln ftp://data.pdbj.org/pub/pdb/validation_reports/tl/8tln | 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: RESIDUE PRO E 51 IS A CIS PROLINE. | ||||||||
Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules E
#1: Protein | Mass: 34362.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin |
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-Non-polymers , 6 types, 165 molecules
#2: Chemical | ChemComp-VAL / | ||||||
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#3: Chemical | ChemComp-LYS / | ||||||
#4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-ZN / | #6: Chemical | ChemComp-DMS / | #7: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | RESIDUES 1321 AND 1322 FORM A DIPEPTIDE (VAL-LYS) BOUND IN THE ACTIVE SITE OF THE MOLECULE. IT IS ...RESIDUES 1321 AND 1322 FORM A DIPEPTIDE (VAL-LYS) BOUND IN THE ACTIVE SITE OF THE MOLECULE. IT IS PRESUMED THAT THE ORIGIN OF THIS DIPEPTIDE IS THE C-TERMINAL TWO RESIDUES OF THE PROTEIN. SINCE THE C-TERMINUS APPEARS AT FULL OCCUPANCY, MOLECULES NOT INCORPORAT |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.29 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.2 / Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.6 Å / Rmerge(I) obs: 0.163 |
-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.6→20 Å / Rfactor obs: 0.165 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.165 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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