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Yorodumi- PDB-1vbj: The crystal structure of prostaglandin F synthase from Trypanosom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vbj | ||||||
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Title | The crystal structure of prostaglandin F synthase from Trypanosoma brucei | ||||||
Components | prostaglandin F synthase | ||||||
Keywords | OXIDOREDUCTASE / TIM BARREL | ||||||
Function / homology | Function and homology information D-arabinose 1-dehydrogenase [NAD(P)+] activity / D-arabinose catabolic process / aldo-keto reductase (NADPH) activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / prostaglandin biosynthetic process / nucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Inoue, T. | ||||||
Citation | Journal: TO BE PUBLISHED Title: The crystal structure of prostaglandin F synthase from Trypanosoma brucei Authors: Inoue, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vbj.cif.gz | 136.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vbj.ent.gz | 106.3 KB | Display | PDB format |
PDBx/mmJSON format | 1vbj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/1vbj ftp://data.pdbj.org/pub/pdb/validation_reports/vb/1vbj | HTTPS FTP |
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-Related structure data
Related structure data | 1mz7 |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31551.115 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Plasmid: PGX4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GV41, prostaglandin-F synthase #2: Chemical | #3: Chemical | #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: 3.46 Å3/Da / Density % sol: 64.45 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 0.68811 Å |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.68811 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. obs: 47485 / % possible obs: 91.1 % / Redundancy: 8.9 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.067 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.248 / Num. unique all: 593 / Rsym value: 0.253 / % possible all: 88.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→32.62 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1451211.5 / 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: 81.1389 Å2 / ksol: 0.350196 e/Å3 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→32.62 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 2.1 Å / Total num. of bins used: 6
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Xplor file |
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