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Yorodumi- PDB-2aim: CRUZAIN INHIBITED WITH BENZOYL-ARGININE-ALANINE-FLUOROMETHYLKETONE -
+Open data
-Basic information
Entry | Database: PDB / ID: 2aim | ||||||
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Title | CRUZAIN INHIBITED WITH BENZOYL-ARGININE-ALANINE-FLUOROMETHYLKETONE | ||||||
Components | CRUZAIN | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / CYSTEINE PROTEASE / TRYPANOSOMA CRUZI / PROTEINASE / PROTEASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information cruzipain / proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / extracellular space Similarity search - Function | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Gillmor, S.A. / Fletterick, R.J. | ||||||
Citation | Journal: Protein Sci. / Year: 1997 Title: Structural determinants of specificity in the cysteine protease cruzain. Authors: Gillmor, S.A. / Craik, C.S. / Fletterick, R.J. #1: Journal: J.Mol.Biol. / Year: 1995 Title: The Crystal Structure of Cruzain: A Therapeutic Target for Chagas' Disease Authors: Mcgrath, M.E. / Eakin, A.E. / Engel, J.C. / Mckerrow, J.H. / Craik, C.S. / Fletterick, R.J. #2: Journal: J.Biol.Chem. / Year: 1993 Title: Production of Crystallizable Cruzain, the Major Cysteine Protease from Trypanosoma Cruzi Authors: Eakin, A.E. / Mcgrath, M.E. / Mckerrow, J.H. / Fletterick, R.J. / Craik, C.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2aim.cif.gz | 63.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2aim.ent.gz | 45.6 KB | Display | PDB format |
PDBx/mmJSON format | 2aim.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2aim_validation.pdf.gz | 509.9 KB | Display | wwPDB validaton report |
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Full document | 2aim_full_validation.pdf.gz | 515.2 KB | Display | |
Data in XML | 2aim_validation.xml.gz | 7 KB | Display | |
Data in CIF | 2aim_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/2aim ftp://data.pdbj.org/pub/pdb/validation_reports/ai/2aim | HTTPS FTP |
-Related 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: 22715.133 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Mutation: GLY 213 STOP Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: TULAHUEN / Cellular location: LYSOSOME, SURFACE / Organelle: LYSOSOME / Plasmid: PLOXCHEYCDELTAC / Cellular location (production host): INCLUSION BODIES / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA References: UniProt: P25779, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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#2: Chemical | ChemComp-ZRA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 33 % | |||||||||||||||
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Crystal grow | Method: vapor diffusion -hanging drop -microseeding / pH: 5 Details: 0.9 M NACITRATE, PH 5.0. CRYSTALS WERE PRODUCED BY MICROSEEDING HANGING DROPS, vapor diffusion -hanging drop -microseeding | |||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop / PH range low: 7 / PH range high: 5 | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jul 1, 1994 |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 8106 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 2.54 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.2→2.35 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 2 / Rsym value: 0.178 / % possible all: 82 |
Reflection shell | *PLUS % possible obs: 82 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CRUZAIN Resolution: 2.2→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.0001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 8.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / 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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