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Yorodumi- PDB-4jbn: Crystal structure of O-Acetyl Serine Sulfhydrylase from Entamoeba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jbn | ||||||
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Title | Crystal structure of O-Acetyl Serine Sulfhydrylase from Entamoeba histolytica in complex with Serine acetyl transferase derived tetrapeptide, SPSI | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Cysteine Synthase / peptide inhibitor / PLP fold type 2 / Tryptophan synthase family / lyase / Serine Acetyl Transferase / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Entamoeba histolytica (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.87 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 | 4jbn.cif.gz | 146 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jbn.ent.gz | 114 KB | Display | PDB format |
PDBx/mmJSON format | 4jbn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/4jbn ftp://data.pdbj.org/pub/pdb/validation_reports/jb/4jbn | HTTPS FTP |
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-Related structure data
Related structure data | 4il5C 4jblC 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: 37136.758 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 #2: Protein/peptide | | Mass: 402.443 Da / Num. of mol.: 1 / Source method: obtained synthetically #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: 2.44 Å3/Da / Density % sol: 49.68 % |
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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: 1.87→27.47 Å / Num. all: 58947 / Num. obs: 58645 / % possible obs: 94.6 % / Observed criterion σ(F): 5.3 / Observed criterion σ(I): 3.6 |
Reflection shell | Resolution: 1.868→1.917 Å / % possible all: 90.77 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PQM Resolution: 1.87→27.47 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.747 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.132 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.2 Å2 / Biso mean: 27.6853 Å2 / Biso min: 11.46 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→27.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.868→1.917 Å / Total num. of bins used: 20
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