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Yorodumi- PDB-6t5x: Crystal structure of Salmonella typhimurium FabG in complex with ... -
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-Basic information
Entry | Database: PDB / ID: 6t5x | ||||||
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Title | Crystal structure of Salmonella typhimurium FabG in complex with NADPH at 1.5 A resolution | ||||||
Components | 3-oxoacyl-[acyl-carrier-protein] reductase FabG | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Fatty acid biosynthesis / FabG / (3-oxoacyl-(Acyl-carrier-protein) reductase) / NADP / NADPH / complex / FAS-II | ||||||
Function / homology | Function and homology information 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid elongation / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / NADP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Vella, P. / Schnell, R. / Schneider, G. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Bioorg.Med.Chem. / Year: 2021 Title: A FabG inhibitor targeting an allosteric binding site inhibits several orthologs from Gram-negative ESKAPE pathogens. Authors: Vella, P. / Rudraraju, R.S. / Lundback, T. / Axelsson, H. / Almqvist, H. / Vallin, M. / Schneider, G. / Schnell, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6t5x.cif.gz | 117.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t5x.ent.gz | 89.3 KB | Display | PDB format |
PDBx/mmJSON format | 6t5x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6t5x_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6t5x_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6t5x_validation.xml.gz | 25.5 KB | Display | |
Data in CIF | 6t5x_validation.cif.gz | 37 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t5/6t5x ftp://data.pdbj.org/pub/pdb/validation_reports/t5/6t5x | HTTPS FTP |
-Related structure data
Related structure data | 6t60C 6t62C 6t65C 6t6nC 6t6pC 6t77C 6t7mC 4afnS 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: 25571.277 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: fabG, STM1195 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0A2C9, 3-oxoacyl-[acyl-carrier-protein] reductase #2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.18 Å3/Da / Density % sol: 43.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M LiSO4 0.1 M HEPES pH 7.5 25 %w/v PEG3350 10 mM NADPH (added to the protein solution) Cryoprotection of the crystals: dipping them in 0.2 M LiSO4 0.1 M HEPES pH 7.5 25 %w/v PEG3350 26% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 27, 2016 / Details: toroidal mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→58.49 Å / Num. obs: 67342 / % possible obs: 95.9 % / Observed criterion σ(I): 2.5 / Redundancy: 2.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.025 / Rpim(I) all: 0.02 / Rrim(I) all: 0.032 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3464 / CC1/2: 0.843 / Rpim(I) all: 0.335 / Rrim(I) all: 0.491 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4AFN Resolution: 1.5→58.21 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.383 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.073 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.33 Å2 / Biso mean: 25.223 Å2 / Biso min: 13.71 Å2
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Refinement step | Cycle: final / Resolution: 1.5→58.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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