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Yorodumi- PDB-1avt: SUBTILISIN CARLSBERG D-PARA-CHLOROPHENYL-1-ACETAMIDO BORONIC ACID... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1avt | ||||||
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Title | SUBTILISIN CARLSBERG D-PARA-CHLOROPHENYL-1-ACETAMIDO BORONIC ACID INHIBITOR COMPLEX | ||||||
Components | SUBTILISIN CARLSBERG, TYPE VIII | ||||||
Keywords | SERINE PROTEASE / HYDROLASE / BORONIC ACID INHIBITORS | ||||||
Function / homology | Function and homology information subtilisin / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus licheniformis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / ISOSTRUCTURAL TO 1SCA / Resolution: 2 Å | ||||||
Authors | Stoll, V.S. / Eger, B.T. / Hynes, R.C. / Martichonok, V. / Jones, J.B. / Pai, E.F. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Differences in binding modes of enantiomers of 1-acetamido boronic acid based protease inhibitors: crystal structures of gamma-chymotrypsin and subtilisin Carlsberg complexes. Authors: Stoll, V.S. / Eger, B.T. / Hynes, R.C. / Martichonok, V. / Jones, J.B. / Pai, E.F. #1: Journal: J.Am.Chem.Soc. / Year: 1996 Title: Probing the Specificity of the Serine Proteases Subtilisin Carlsberg and A-Chymotrypsin with Enantiomeric 1-Acetamido Boronic Acids. An Unexpected Reversal of the Normal "L"-Stereoselectivity Preference Authors: Martichonok, V. / Jones, J.B. #2: Journal: Bioorg.Med.Chem. / Year: 1994 Title: Probing the Specificity of the S1 Binding Site of Subtilisin Carlsberg with Boronic Acids Authors: Seufer-Wasserthal, P. / Martichonok, V. / Keller, T.H. / Chin, B. / Martin, R. / Jones, J.B. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993 Title: Enzyme Crystal Structure in a Neat Organic Solvent Authors: Fitzpatrick, P.A. / Steinmetz, A.C. / Ringe, D. / Klibanov, A.M. #4: Journal: J.Mol.Biol. / Year: 1976 Title: The Structure of Subtilopeptidase A. I. X-Ray Crystallographic Data Authors: Petsko, G.A. / Tsernoglou, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1avt.cif.gz | 61.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1avt.ent.gz | 47.2 KB | Display | PDB format |
PDBx/mmJSON format | 1avt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/1avt ftp://data.pdbj.org/pub/pdb/validation_reports/av/1avt | HTTPS FTP |
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-Related structure data
Related structure data | 1av7C 1vgcC 1vsbC 2vgcC 3vgcC 3vsbC 4vgcC 1scaS 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
#1: Protein | Mass: 27546.670 Da / Num. of mol.: 1 / Fragment: FULL PROTEIN / Source method: isolated from a natural source / Details: PURCHASED FROM SIGMA / Source: (natural) Bacillus licheniformis (bacteria) / References: UniProt: P00780, subtilisin | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 7 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 41.5 % Description: THE COORDINATES OF THE STARTING MODEL WERE RE-INDEXED TO CONFORM TO AXIS LABELING CONVENTION A | Crystal grow | pH: 7 / Details: AS GIVEN IN REFERENCE 4, pH 7.0 | |||||||||||||
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Crystal grow | *PLUS pH: 5.6 / Method: batch method / Details: Petsko, G.A., (1976) J.Mol.Biol., 106, 453. | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Nov 1, 1993 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 15092 / % possible obs: 96 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2→2.09 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.083 / Mean I/σ(I) obs: 7 / Rsym value: 0.083 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: ISOSTRUCTURAL TO 1SCA Starting model: PDB ENTRY 1SCA Resolution: 2→8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: INDIVIDUAL / Cross valid method: THROUGHOUT / σ(F): 1
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Displacement parameters | Biso mean: 12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.227 |