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Yorodumi- PDB-2oz2: Crystal structure analysis of cruzain bound to vinyl sulfone deri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2oz2 | ||||||
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Title | Crystal structure analysis of cruzain bound to vinyl sulfone derived inhibitor (K11777) | ||||||
Components | Cruzipain | ||||||
Keywords | HYDROLASE / CYSTEINE PROTEASE / COVALENT INHIBITOR / VINYL SULFONEAMIDE DERIVED | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Rickert, M. / Brinen, L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Vinyl sulfones as antiparasitic agents and a structural basis for drug design. Authors: Kerr, I.D. / Lee, J.H. / Farady, C.J. / Marion, R. / Rickert, M. / Sajid, M. / Pandey, K.C. / Caffrey, C.R. / Legac, J. / Hansell, E. / McKerrow, J.H. / Craik, C.S. / Rosenthal, P.J. / Brinen, L.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oz2.cif.gz | 94.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oz2.ent.gz | 77 KB | Display | PDB format |
PDBx/mmJSON format | 2oz2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oz/2oz2 ftp://data.pdbj.org/pub/pdb/validation_reports/oz/2oz2 | 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: 22715.133 Da / Num. of mol.: 2 / Fragment: CRUZAIN (Residues 123-337) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Plasmid: pCheY15LOX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P25779, cruzipain #2: Chemical | ChemComp-SO4 / #3: Chemical | #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: 2.43 Å3/Da / Density % sol: 49.44 % |
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Crystal grow | Temperature: 291.15 K / pH: 6 Details: pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→70 Å / Num. obs: 34896 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 4.7 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→35.01 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.224 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.144 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.23 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→35.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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