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Yorodumi- PDB-1qf1: THERMOLYSIN (E.C.3.4.24.27) COMPLEXED WITH (2-SULPHANYLHEPTANOYL)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qf1 | ||||||
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Title | THERMOLYSIN (E.C.3.4.24.27) COMPLEXED WITH (2-SULPHANYLHEPTANOYL)-PHE-ALA. PARAMETERS FOR ZN-BIDENTATION OF MERCAPTOACYLDIPEPTIDES IN METALLOENDOPEPTIDASE | ||||||
Components | PROTEIN (THERMOLYSIN) | ||||||
Keywords | HYDROLASE / NEUTRAL ENDOPEPTIDASE / ZN METALLOPEPTIDASE | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Gaucher, J.-F. / Selkti, M. / Tiraboschi, G. / Prange, T. / Roques, B.P. / Tomas, A. / Fournie-Zaluski, M.C. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Crystal structures of alpha-mercaptoacyldipeptides in the thermolysin active site: structural parameters for a Zn monodentation or bidentation in metalloendopeptidases. Authors: Gaucher, J.F. / Selkti, M. / Tiraboschi, G. / Prange, T. / Roques, B.P. / Tomas, A. / Fournie-Zaluski, M.C. #1: Journal: J.Med.Chem. / Year: 1996 Title: Design of orally active dual inhibitors of neutral endopeptidase and angiotensin-converting enzyme with long duration of action. Authors: Fournie-Zaluski, M.C. / Coric, P. / Thery, V. / Gonzalez, W. / Meudal, H. / Turcaud, S. / Michel, J.B. / Roques, B.P. #2: Journal: J.Med.Chem. / Year: 1996 Title: Optimal recognition of neutral endopeptidase and angiotensin-converting enzyme active sites by mercaptoacyldipeptides as a means to design potent dual inhibitors. Authors: Coric, P. / Turcaud, S. / Meudal, H. / Roques, B.P. / Fournie-Zaluski, M.C. #3: Journal: Protein Sci. / Year: 1995 Title: Structural analysis of zinc substitutions in the active site of thermolysin. Authors: Holland, D.R. / Hausrath, A.C. / Juers, D. / Matthews, B.W. #4: 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. / Dupourque, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qf1.cif.gz | 82.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qf1.ent.gz | 59.6 KB | Display | PDB format |
PDBx/mmJSON format | 1qf1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qf1_validation.pdf.gz | 734.8 KB | Display | wwPDB validaton report |
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Full document | 1qf1_full_validation.pdf.gz | 735 KB | Display | |
Data in XML | 1qf1_validation.xml.gz | 15 KB | Display | |
Data in CIF | 1qf1_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qf/1qf1 ftp://data.pdbj.org/pub/pdb/validation_reports/qf/1qf1 | HTTPS FTP |
-Related structure data
Related structure data | 1qf0C 1qf2C 1lnfS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#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 , 5 types, 212 molecules
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-TI1 / [ | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | CATALYTIC ZN |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 40 % |
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Crystal grow | pH: 8 / Details: pH 8.0 |
Crystal grow | *PLUS Method: other / Details: Matthews, B.W., (1972) Nat. New. Biol., 238, 37. |
-Data collection
Diffraction | Mean temperature: 278 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.97 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2→23.4 Å / Num. obs: 23624 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Redundancy: 3.4 % / Biso Wilson estimate: 16.6 Å2 / Rsym value: 0.093 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2→2.23 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.26 / % possible all: 99 |
Reflection | *PLUS Rmerge(I) obs: 0.093 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LNF Resolution: 2→10 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: THE WHOLE SET OF DATA WAS USED FOR THE LAST STEPS OF REFINEMENT (ENERGY MINIMIZATION, B-REFINEMENT). CONSEQUENTLY FREE RVALUE WAS CALCULATED BEFORE THIS STEPS.
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Displacement parameters | Biso mean: 10.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.165 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 12.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.25 / % reflection Rfree: 10 % / Rfactor Rwork: 0.199 |