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Yorodumi- PDB-6t6n: Crystal structure of Klebsiella pneumoniae FabG2(NADH-dependent) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t6n | ||||||
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Title | Crystal structure of Klebsiella pneumoniae FabG2(NADH-dependent) in complex with NADH at 2.5 A resolution | ||||||
Components | 3-oxoacyl-[acyl-carrier protein] reductase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Fatty acid biosynthesis / FabG / (3-oxoacyl-(Acyl-carrier-protein) reductase) / NADH / NADPH / complex / FAS-II | ||||||
Function / homology | 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / D-MALATE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / 3-oxoacyl-[acyl-carrier protein] reductase Function and homology information | ||||||
Biological species | Klebsiella pneumoniae 30684/NJST258_2 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Vella, P. / Schnell, R. / Lindqvist, Y. / 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 | 6t6n.cif.gz | 376.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t6n.ent.gz | 311.1 KB | Display | PDB format |
PDBx/mmJSON format | 6t6n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6t6n_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 6t6n_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 6t6n_validation.xml.gz | 71.1 KB | Display | |
Data in CIF | 6t6n_validation.cif.gz | 94.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t6/6t6n ftp://data.pdbj.org/pub/pdb/validation_reports/t6/6t6n | HTTPS FTP |
-Related structure data
Related structure data | 6t5xC 6t60C 6t62C 6t65C 6t6pC 6t77C 6t7mC 4jroS 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 25643.330 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: FabG2 from Klebsiella pneumoniae is a homologue of the fatty acid bisynthesis enzyme FabG, however NADH-dependent. It catalyses the reduction of 3-oxo-acyl(C4)-CoA substrate. Source: (gene. exp.) Klebsiella pneumoniae 30684/NJST258_2 (bacteria) Gene: KPNJ2_02761 / Plasmid: pNIC28-Bsa4 Details (production host): N-terminal His6-tag, removable by TEV cleavage Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: W8VGR4, 3-oxoacyl-[acyl-carrier-protein] reductase #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-NAI / #4: Chemical | ChemComp-MLT / | #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: 3.24 Å3/Da / Density % sol: 0.63 % / Description: short rods |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20 % PEG3350 0.2 M Na malonate pH 6.0 12.5 mM NADH added to the protein solution prior to drop mixing |
-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 mirrors |
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: 2.5→48.96 Å / Num. obs: 92045 / % possible obs: 99.3 % / Redundancy: 4.3 % / Biso Wilson estimate: 46.1 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.044 / Rrim(I) all: 0.096 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4546 / CC1/2: 0.739 / Rpim(I) all: 0.369 / Rrim(I) all: 0.779 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JRO Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.956 / SU B: 8.554 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.368 / ESU R Free: 0.224 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: 135.51 Å2 / Biso mean: 55.47 Å2 / Biso min: 13.29 Å2
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Refinement step | Cycle: final / Resolution: 2.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.564 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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