+Open data
-Basic information
Entry | Database: PDB / ID: 6vlx | |||||||||
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Title | Crystal structure of FabI from Alistipes finegoldii | |||||||||
Components | Enoyl-[acyl-carrier-protein] reductase [NADH] | |||||||||
Keywords | OXIDOREDUCTASE / Enoyl-ACP Reductase / FabI | |||||||||
Function / homology | enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / Enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / NAD(P)-binding domain superfamily / Enoyl-[acyl-carrier-protein] reductase [NADH] Function and homology information | |||||||||
Biological species | Alistipes finegoldii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | |||||||||
Authors | Radka, C.D. / Seetharaman, J. / Rock, C.O. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: The genome of a Bacteroidetes inhabitant of the human gut encodes a structurally distinct enoyl-acyl carrier protein reductase (FabI). Authors: Radka, C.D. / Frank, M.W. / Yao, J. / Seetharaman, J. / Miller, D.J. / Rock, C.O. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vlx.cif.gz | 126.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vlx.ent.gz | 95.2 KB | Display | PDB format |
PDBx/mmJSON format | 6vlx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vlx_validation.pdf.gz | 265.5 KB | Display | wwPDB validaton report |
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Full document | 6vlx_full_validation.pdf.gz | 265.5 KB | Display | |
Data in XML | 6vlx_validation.xml.gz | 1.1 KB | Display | |
Data in CIF | 6vlx_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vl/6vlx ftp://data.pdbj.org/pub/pdb/validation_reports/vl/6vlx | HTTPS FTP |
-Related structure data
Related structure data | 6vlyC 2p91S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 34131.625 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alistipes finegoldii (bacteria) / Gene: fabI, ERS852447_01935 / Production host: Escherichia coli (E. coli) References: UniProt: A0A174E195, enoyl-[acyl-carrier-protein] reductase (NADH) #2: Chemical | ChemComp-GOL / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.2 Å3/Da / Density % sol: 44.1 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: Crystallization: 1.2 M Na K Tartrate, 100 mM Tris pH 8.0, Cryo: 1.3M Na K Tartrate, 100 mM Tris pH 8.0, 20% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 12, 2018 Details: Si 111. Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror |
Radiation | Monochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→35 Å / Num. obs: 62918 / % possible obs: 98.3 % / Redundancy: 6.4 % / CC1/2: 0.997 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.72→1.76 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2748 / CC1/2: 0.909 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2P91 Resolution: 1.72→29.52 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.377 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.119 / 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: 134.68 Å2 / Biso mean: 32.048 Å2 / Biso min: 14.37 Å2
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Refinement step | Cycle: final / Resolution: 1.72→29.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.725→1.769 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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