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Yorodumi- PDB-4gie: Crystal structure of prostaglandin F synthase from Trypanosoma cr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gie | ||||||
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Title | Crystal structure of prostaglandin F synthase from Trypanosoma cruzi bound to NADP | ||||||
Components | Prostaglandin F synthase | ||||||
Keywords | OXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Chagas disease / prostaglandin D2 / trypanosomiasis / eukaryotic pathogen / parasite / NADP+ / NADPH / Rutin / Bimatoprost | ||||||
Function / homology | Function and homology information prostaglandin H2 endoperoxidase reductase 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 cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015 Title: Structures of prostaglandin F synthase from the protozoa Leishmania major and Trypanosoma cruzi with NADP. Authors: Moen, S.O. / Fairman, J.W. / Barnes, S.R. / Sullivan, A. / Nakazawa-Hewitt, S. / Van Voorhis, W.C. / Staker, B.L. / Lorimer, D.D. / Myler, P.J. / Edwards, T.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gie.cif.gz | 149.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gie.ent.gz | 115.2 KB | Display | PDB format |
PDBx/mmJSON format | 4gie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gie_validation.pdf.gz | 714.7 KB | Display | wwPDB validaton report |
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Full document | 4gie_full_validation.pdf.gz | 715.1 KB | Display | |
Data in XML | 4gie_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 4gie_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/4gie ftp://data.pdbj.org/pub/pdb/validation_reports/gi/4gie | HTTPS FTP |
-Related structure data
Related structure data | 4f40C 4fziSC 4g5dC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33592.035 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: CL Brener / Gene: Tc00.1047053511287.49 / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4DJ07, prostaglandin-F synthase |
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#2: Chemical | ChemComp-ACT / |
#3: Chemical | ChemComp-NAP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.71 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: TrcrA.00019.a.B1 at 20 mg/mL with 2 mM NADP against Index G6: 0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, 25% PEG3350, cryoprotectant: 15% ethylene glycol, crystal tracking ID 235869g6, ...Details: TrcrA.00019.a.B1 at 20 mg/mL with 2 mM NADP against Index G6: 0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, 25% PEG3350, cryoprotectant: 15% ethylene glycol, crystal tracking ID 235869g6, unique puck ID pzu9-6, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 27, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.25→50 Å / Num. all: 80172 / Num. obs: 75887 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 12.33 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 23.41 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4FZI Resolution: 1.25→29.87 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.975 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 0.86 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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: 44.76 Å2 / Biso mean: 9.0386 Å2 / Biso min: 2.73 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→29.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.25→1.282 Å / Total num. of bins used: 20
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