+Open data
-Basic information
Entry | Database: PDB / ID: 3atz | ||||||
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Title | Crystal structure of TcOYE with pHBA | ||||||
Components | Prostaglandin F2a synthase | ||||||
Keywords | Oxidoreductase/Oxidoreductase inhibitor / alpha/beta barrel / flavin mononucleotide / Oxidoreductase-Oxidoreductase inhibitor complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å | ||||||
Authors | Okamoto, N. / Yamaguchi, K. / Mizohata, E. / Tokuoka, K. / Uchiyama, N. / Sugiyama, S. / Matsumura, H. / Inaka, K. / Urade, Y. / Inoue, T. | ||||||
Citation | Journal: J.Biochem. / Year: 2011 Title: Structural insight into the stereoselective production of PGF2(alpha) by Old Yellow Enzyme from Trypanosoma cruzi Authors: Okamoto, N. / Yamaguchi, K. / Mizohata, E. / Tokuoka, K. / Uchiyama, N. / Sugiyama, S. / Matsumura, H. / Inaka, K. / Urade, Y. / Inoue, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3atz.cif.gz | 310.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3atz.ent.gz | 251.9 KB | Display | PDB format |
PDBx/mmJSON format | 3atz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/3atz ftp://data.pdbj.org/pub/pdb/validation_reports/at/3atz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 42312.836 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: TcPGFS / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8I6L9 #2: Chemical | ChemComp-FMN / #3: Chemical | ChemComp-HBA / #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: 1.86 Å3/Da / Density % sol: 34.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 2000, Ammonium fluoride, Urea, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Jun 29, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.04→50 Å / Num. obs: 78333 / % possible obs: 100 % / Biso Wilson estimate: 14.5 Å2 |
Reflection shell | Resolution: 2.05→2.12 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→37.18 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 319756.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.9481 Å2 / ksol: 0.338905 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.04→37.18 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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