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Yorodumi- PDB-6t7m: Crystal structure of Salmonella typhimurium FabG at 2.65 A resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t7m | ||||||
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Title | Crystal structure of Salmonella typhimurium FabG at 2.65 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: 2.65 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 | 6t7m.cif.gz | 190.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t7m.ent.gz | 152.3 KB | Display | PDB format |
PDBx/mmJSON format | 6t7m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6t7m_validation.pdf.gz | 458.7 KB | Display | wwPDB validaton report |
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Full document | 6t7m_full_validation.pdf.gz | 471.3 KB | Display | |
Data in XML | 6t7m_validation.xml.gz | 36.8 KB | Display | |
Data in CIF | 6t7m_validation.cif.gz | 51.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t7/6t7m ftp://data.pdbj.org/pub/pdb/validation_reports/t7/6t7m | HTTPS FTP |
-Related structure data
Related structure data | 6t5xC 6t60C 6t62C 6t65C 6t6nC 6t6pC 6t77C 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: 28130.027 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: N-terminal His6-tag (Sequence: MHHHHHHSSGVDLGTENLYFQS) Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: fabG, STM1195 / Plasmid: pNIC28Bsa4 Details (production host): N-terminal His6-tag (Sequence: MHHHHHHSSGVDLGTENLYFQS) Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0A2C9, 3-oxoacyl-[acyl-carrier-protein] reductase #2: 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: 2.57 Å3/Da / Density % sol: 52.09 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Bis-Tris propane pH 8.50 2 M Sodium Sulfate 20% w/v PEG3350 2% Glycerol Cryoprotection PEG 400 25% included to the Mother liquor: crystals diped in a drop |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 21, 2014 / Details: Sagittally bended Si111 crystal |
Radiation | Monochromator: Double crystal (Si, 111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→48.063 Å / Num. obs: 34344 / % possible obs: 99.9 % / Redundancy: 3.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.062 / Rrim(I) all: 0.122 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.65→2.78 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4516 / CC1/2: 0.642 / Rpim(I) all: 0.598 / Rrim(I) all: 0.906 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4AFN Resolution: 2.65→48.063 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.85
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.44 Å2 / Biso mean: 53.9141 Å2 / Biso min: 25.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.65→48.063 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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