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Yorodumi- PDB-4xui: Crystal structure analysis of cruzain bound to the no-covalent an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xui | |||||||||
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Title | Crystal structure analysis of cruzain bound to the no-covalent analog of WRR-483 (WRR-669) | |||||||||
Components | Cruzipain | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Cruzain / cysteine protease / covalent reversible inhibitor / Chagas Disease / Trypanosoma cruzi / vinyl sulfone analog / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Trypanosoma cruzi (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.508 Å | |||||||||
Authors | Tochowicz, A. / McKerrow, J.H. | |||||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2016 Title: Synthesis and Evaluation of Oxyguanidine Analogues of the Cysteine Protease Inhibitor WRR-483 against Cruzain. Authors: Jones, B.D. / Tochowicz, A. / Tang, Y. / Cameron, M.D. / McCall, L.I. / Hirata, K. / Siqueira-Neto, J.L. / Reed, S.L. / McKerrow, J.H. / Roush, W.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xui.cif.gz | 133.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xui.ent.gz | 104.4 KB | Display | PDB format |
PDBx/mmJSON format | 4xui.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/4xui ftp://data.pdbj.org/pub/pdb/validation_reports/xu/4xui | HTTPS FTP |
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-Related structure data
Related structure data | 4pi3C 3kkuS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 22772.186 Da / Num. of mol.: 3 / Fragment: UNP residues 122-337 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: P25779, cruzipain #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.6 M Ammonium Sulfate, 0.1 M Sodium chloride and 0.1 M HEPES |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 25397 / % possible obs: 99.1 % / Redundancy: 5.1 % / Biso Wilson estimate: 25.77 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 14.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KKU Resolution: 2.508→29.504 Å / Cross valid method: FREE R-VALUE / σ(F): 2.08 / Phase error: 17.68 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.508→29.504 Å
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Refine LS restraints |
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LS refinement shell |
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