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Yorodumi- PDB-2y6t: Molecular Recognition of Chymotrypsin by the Serine Protease Inhi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y6t | ||||||
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Title | Molecular Recognition of Chymotrypsin by the Serine Protease Inhibitor Ecotin from Yersinia pestis | ||||||
Components |
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Keywords | HYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information chymotrypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / periplasmic space / serine-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | YERSINIA PSEUDOTUBERCULOSIS (bacteria) BOS TAURUS (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å | ||||||
Authors | Clark, E.A. / Walker, N. / Ford, D.C. / Cooper, I.A. / Oyston, P.C.F. / Acharya, K.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Molecular Recognition of Chymotrypsin by the Serine Protease Inhibitor Ecotin from Yersinia Pestis. Authors: Clark, E.A. / Walker, N. / Ford, D.C. / Cooper, I.A. / Oyston, P.C. / Acharya, K.R. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y6t.cif.gz | 286.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y6t.ent.gz | 233.1 KB | Display | PDB format |
PDBx/mmJSON format | 2y6t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/2y6t ftp://data.pdbj.org/pub/pdb/validation_reports/y6/2y6t | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25686.037 Da / Num. of mol.: 4 / Source method: isolated from a natural source Details: ACTIVATED BOVINE CHYMOTRYPSIN WAS PURCHASED FROM SIGMA-ALDRICH Source: (natural) BOS TAURUS (cattle) / References: UniProt: P00766, chymotrypsin #2: Protein | Mass: 16747.180 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) YERSINIA PSEUDOTUBERCULOSIS (bacteria) / Strain: YPIII / Plasmid: PCRT7/NT-TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: B1JSA0 #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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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: 2.17 Å3/Da / Density % sol: 43.5 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: RESERVOIR SOLUTION - 100 MM BIS TRIS PH 5.5, 200 MM AMMONIUM SULPHATE, 17.5% PEG3350. PROTEIN SOLUTION - 3 MG/ML ECOTIN, 6 MG/ML CHYMOTRYPSIN IN 5MM TRIS PH 7.5. DROP - 1:1 VOLUME RATIO RESERVOIR:PROTEIN. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.978 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 20, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.74→169.48 Å / Num. obs: 42247 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 54.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.27 |
Reflection shell | Resolution: 2.74→2.84 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.51 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 4CHA AND 1ECZ Resolution: 2.74→169.48 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.824 / SU B: 18.243 / SU ML: 0.367 / Cross valid method: THROUGHOUT / ESU R Free: 0.48 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.89 Å2
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Refinement step | Cycle: LAST / Resolution: 2.74→169.48 Å
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