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Yorodumi- PDB-4tln: BINDING OF HYDROXAMIC ACID INHIBITORS TO CRYSTALLINE THERMOLYSIN ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4tln | |||||||||
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Title | BINDING OF HYDROXAMIC ACID INHIBITORS TO CRYSTALLINE THERMOLYSIN SUGGESTS A PENTACOORDINATE ZINC INTERMEDIATE IN 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 / MOLECULAR SUBSTATUTION / Resolution: 2.3 Å | |||||||||
Authors | Matthews, B.W. / Holmes, M.A. | |||||||||
Citation | 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. #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: 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. #4: Journal: J.Biol.Chem. / Year: 1977 Title: Comparison of the Structures of Carboxypeptidase a and Thermolysin Authors: Kester, W.R. / Matthews, B.W. #5: 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. #6: 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. #7: Journal: Biochemistry / Year: 1976 Title: Role of Calcium in the Thermal Stability of Thermolysin Authors: Dahlquist, F.W. / Long, J.W. / Bigbee, W.L. #8: 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. #9: Journal: J.Biol.Chem. / Year: 1974 Title: The Conformation of Thermolysin Authors: Matthews, B.W. / Weaver, L.H. / Kester, W.R. #10: Journal: Biochemistry / Year: 1974 Title: Binding of Lanthanide Ions to Thermolysin Authors: Matthews, B.W. / Weaver, L.H. #11: 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. #12: 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. #13: 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. #14: 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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Remark 700 | SHEET THE *ACTIVE-SITE* SHEET SUBSTRUCTURE OF THIS MOLECULE HAS ONE EDGE-STRAND COMPRISED OF TWO ...SHEET THE *ACTIVE-SITE* SHEET SUBSTRUCTURE OF THIS MOLECULE HAS ONE EDGE-STRAND COMPRISED OF TWO DISTINCT SEQUENCES OF THE POLYPEPTIDE CHAIN. TO REPRESENT THIS FEATURE AN EXTRA SHEET IS DEFINED. STRANDS 2,3,4,5 OF S1 ARE IDENTICAL TO STRANDS 2,3,4,5 OF S2. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4tln.cif.gz | 85.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tln.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 4tln.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4tln_validation.pdf.gz | 443.9 KB | Display | wwPDB validaton report |
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Full document | 4tln_full_validation.pdf.gz | 496.5 KB | Display | |
Data in XML | 4tln_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | 4tln_validation.cif.gz | 30.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/4tln ftp://data.pdbj.org/pub/pdb/validation_reports/tl/4tln | 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: RESIDUE 51 IS A CIS-PROLINE. |
-Components
#1: Protein | Mass: 34362.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus thermoproteolyticus (bacteria) References: UniProt: P00800, thermolysin | ||||||
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#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-LNO / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.76 % / Description: data collected with precession photography | ||||||||||||||||||||
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Crystal grow | pH: 7.2 / Details: pH 7.2 | ||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 285 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-3 / Wavelength: 1.54 |
Detector | Type: KODAK / Detector: FILM / Date: 1980 / Details: ADJUSTABLE COLLIMATOR SLIT |
Radiation | Monochromator: NICKEL FILTER / Protocol: SINGLE CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→26.6 Å / Num. obs: 12029 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.026 / Rsym value: 0.063 |
Reflection | *PLUS Highest resolution: 2.3 Å / Num. obs: 12029 / Rmerge(I) obs: 0.026 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR SUBSTATUTION / Resolution: 2.3→10 Å / Cross valid method: NONE / σ(F): 0 / Stereochemistry target values: TNT PROTGEO VERSION 1.0 Details: ATOM 2448 IN HET GROUP *LNO* IS AN OXYGEN ATOM AND IS IDENTIFIED IN THIS ENTRY AS * ON2*. IN THE PAPER CITED IN THE JRNL RECORDS ABOVE IT IS IDENTIFIED AS * N2O*.
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Solvent computation | Solvent model: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 10 Å / Num. reflection obs: 11854 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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