+Open data
-Basic information
Entry | Database: PDB / ID: 5u5g | ||||||
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Title | Psf3 in complex with NADP+ and 2-OPP | ||||||
Components | 6-phosphogluconate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Fosfomycin / Reductase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas syringae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.048 Å | ||||||
Authors | Olivares, P. / Nair, S.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: ACS Chem. Biol. / Year: 2017 Title: Characterization of Two Late-Stage Enzymes Involved in Fosfomycin Biosynthesis in Pseudomonads. Authors: Olivares, P. / Ulrich, E.C. / Chekan, J.R. / van der Donk, W.A. / Nair, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5u5g.cif.gz | 246.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u5g.ent.gz | 198.1 KB | Display | PDB format |
PDBx/mmJSON format | 5u5g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u5/5u5g ftp://data.pdbj.org/pub/pdb/validation_reports/u5/5u5g | HTTPS FTP |
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-Related 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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Details | Dimer as determined by Size Exclusion Chromatography |
-Components
#1: Protein | Mass: 31597.094 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas syringae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: I6R485 #2: Chemical | ChemComp-NAP / #3: Chemical | ChemComp-7VD / ( #4: Chemical | #5: 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: 2.61 Å3/Da / Density % sol: 52.88 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 12 mg/mL Psf3, 43% v/v polypropylene glycol P400, 0.1 M Bis-Tris Methane pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 8, 2014 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 78862 / % possible obs: 96.6 % / Redundancy: 3.5 % / Rsym value: 0.124 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 2 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.048→46.324 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.048→46.324 Å
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Refine LS restraints |
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LS refinement shell |
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