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Yorodumi- PDB-4il5: Crystal structure of O-Acetyl Serine Sulfhydrylase from Entamoeba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4il5 | ||||||
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Title | Crystal structure of O-Acetyl Serine Sulfhydrylase from Entamoeba histolytica in complex with isoleucine | ||||||
Components | Cysteine synthase | ||||||
Keywords | TRANSFERASE / O-Acetyl Serine Sulfhydrylase / Cysteine Synthase / fold type II PLP dependent enzyme / lyase / Serine acetyl transferase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Entamoeba histolytica (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | ||||||
Authors | Raj, I. / Gourinath, S. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2013 Title: Molecular basis of ligand recognition by OASS from E. histolytica: insights from structural and molecular dynamics simulation studies Authors: Raj, I. / Mazumder, M. / Gourinath, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4il5.cif.gz | 142.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4il5.ent.gz | 112.9 KB | Display | PDB format |
PDBx/mmJSON format | 4il5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/il/4il5 ftp://data.pdbj.org/pub/pdb/validation_reports/il/4il5 | HTTPS FTP |
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-Related structure data
Related structure data | 4jblC 4jbnC 2pqmS 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: 36998.613 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM-1:IMSS / Gene: EhOASS / Plasmid: pET21c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O15570, cysteine synthase #2: Chemical | ChemComp-ILE / | #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: 2.46 Å3/Da / Density % sol: 49.97 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 2.1M AmSO4, 150mM NaCl, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 30, 2008 |
Radiation | Monochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→30 Å / Num. obs: 45105 / % possible obs: 97.4 % / Observed criterion σ(F): 10.7 / Observed criterion σ(I): 3 |
Reflection shell | Resolution: 2.03→2.11 Å / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PQM Resolution: 2.03→27.57 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.828 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.188 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
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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 max: 82.2 Å2 / Biso mean: 27.5994 Å2 / Biso min: 12.02 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→27.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.034→2.087 Å / Total num. of bins used: 20
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