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Yorodumi- PDB-1hyt: RE-DETERMINATION AND REFINEMENT OF THE COMPLEX OF BENZYLSUCCINIC ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hyt | ||||||
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Title | RE-DETERMINATION AND REFINEMENT OF THE COMPLEX OF BENZYLSUCCINIC ACID WITH THERMOLYSIN AND ITS RELATION TO THE COMPLEX WITH CARBOXYPEPTIDASE A | ||||||
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 SUBSTITUTION / Resolution: 1.7 Å | ||||||
Authors | Hausrath, A.C. / Matthews, B.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1994 Title: Redetermination and refinement of the complex of benzylsuccinic acid with thermolysin and its relation to the complex with carboxypeptidase A. Authors: Hausrath, A.C. / Matthews, B.W. #1: Journal: Biochemistry / Year: 1984 Title: Binding of N-Carboxymethyl Dipeptide Inhibitors to Thermolysin Determined by X-Ray Crystallography: A Novel Class of Transition-State Analogues for Zinc Peptidases Authors: Monzingo, A.F. / Matthews, B.W. #2: Journal: J.Mol.Biol. / Year: 1982 Title: Structure of Thermolysin Refined at 1.6 Angstroms Resolution Authors: Holmes, M.A. / Matthews, B.W. #3: Journal: J.Biol.Chem. / Year: 1974 Title: The Conformation of Thermolysin Authors: Matthews, B.W. / Weaver, L.H. / Kester, W.R. #4: 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. #5: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hyt.cif.gz | 79.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hyt.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 1hyt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hyt_validation.pdf.gz | 440.8 KB | Display | wwPDB validaton report |
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Full document | 1hyt_full_validation.pdf.gz | 445 KB | Display | |
Data in XML | 1hyt_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 1hyt_validation.cif.gz | 22 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/1hyt ftp://data.pdbj.org/pub/pdb/validation_reports/hy/1hyt | HTTPS FTP |
-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: CIS PROLINE - PRO 51 |
-Components
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 5 types, 164 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-DMS / | #5: Chemical | ChemComp-BZS / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.25 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.2 / Details: pH 7.2 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown / Details: Holmes, M.A., (1982) J.Mol.Biol., 160, 623. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN / Detector: MULTIWIRE AREA DETECTOR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.7 Å / Num. obs: 35931 / % possible obs: 94 % / Rmerge(I) obs: 0.045 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR SUBSTITUTION / Resolution: 1.7→20 Å / σ(F): 4 /
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.157 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 30.1 Å2 | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_angle_d / Dev ideal: 1.9 |