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- PDB-8jfg: Crystal structure of 3-oxoacyl-ACP reductase FabG in complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8jfg | ||||||
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Title | Crystal structure of 3-oxoacyl-ACP reductase FabG in complex with NADP+ and 3-keto-octanoyl-ACP from Helicobacter pylori | ||||||
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![]() | BIOSYNTHETIC PROTEIN / 3-oxoacyl-ACP reductase / FabG / NADP+ / 3-keto-octanoyl-ACP / Helicobacter pylori | ||||||
Function / homology | ![]() Kdo2-lipid A biosynthetic process / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / lipid A biosynthetic process / phosphopantetheine binding / acyl binding / acyl carrier activity / fatty acid biosynthetic process / NAD binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhou, J.S. / Zhang, L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The Molecular Basis of Catalysis by SDR Family Members Ketoacyl-ACP Reductase FabG and Enoyl-ACP Reductase FabI in Type-II Fatty Acid Biosynthesis. Authors: Zhou, J. / Zhang, L. / Wang, Y. / Song, W. / Huang, Y. / Mu, Y. / Schmitz, W. / Zhang, S.Y. / Lin, H. / Chen, H.Z. / Ye, F. / Zhang, L. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 295.4 KB | Display | ![]() |
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PDB format | ![]() | 241.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
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Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 63.8 KB | Display | |
Data in CIF | ![]() | 82.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8jf9SC ![]() 8jfaC ![]() 8jfhC ![]() 8jfiC ![]() 8jfjC ![]() 8jfmC ![]() 8jfnC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26768.533 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: G2M827, 3-oxoacyl-[acyl-carrier-protein] reductase #2: Protein | | Mass: 8566.640 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-NAP / #4: Chemical | ChemComp-UHC / ~{ | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.5 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Imidazole pH 7.0, 30% v/v MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9875 Å / Relative weight: 1 |
Reflection | Resolution: 2.83→41.56 Å / Num. obs: 41901 / % possible obs: 99 % / Redundancy: 7.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.057 / Rrim(I) all: 0.157 / Χ2: 0.98 / Net I/σ(I): 11.8 / Num. measured all: 310751 |
Reflection shell | Resolution: 2.83→2.9 Å / % possible obs: 99.4 % / Redundancy: 7.6 % / Rmerge(I) obs: 1.84 / Num. measured all: 23303 / Num. unique obs: 3070 / CC1/2: 0.707 / Rpim(I) all: 0.705 / Rrim(I) all: 1.974 / Χ2: 0.95 / Net I/σ(I) obs: 1.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8JF9 Resolution: 2.83→41.56 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.81 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.83→41.56 Å
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Refine LS restraints |
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LS refinement shell |
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