[English] 日本語
Yorodumi- PDB-8jfn: Crystal structure of enoyl-ACP reductase FabI in complex with NAD... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jfn | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of enoyl-ACP reductase FabI in complex with NAD+ and crotonyl-ACP from Helicobacter pylori | ||||||
Components |
| ||||||
Keywords | BIOSYNTHETIC PROTEIN / enoyl-ACP reductase / FabI / NAD+ / crotonyl-ACP / Helicobacter pylori | ||||||
Function / homology | Function and homology information Kdo2-lipid A biosynthetic process / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / phosphopantetheine binding / acyl carrier activity / fatty acid biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å | ||||||
Authors | Song, W.Y. / Zhang, L. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2023 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. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8jfn.cif.gz | 86.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8jfn.ent.gz | 62.3 KB | Display | PDB format |
PDBx/mmJSON format | 8jfn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/8jfn ftp://data.pdbj.org/pub/pdb/validation_reports/jf/8jfn | HTTPS FTP |
---|
-Related structure data
Related structure data | 8jf9C 8jfaC 8jfgC 8jfhC 8jfiC 8jfjC 8jfmSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 29746.154 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: fabI / Production host: Escherichia coli (E. coli) / References: UniProt: A0A086RSH0 |
---|---|
#2: Protein | Mass: 8740.794 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: acpP / Production host: Escherichia coli (E. coli) / References: UniProt: Q5EDC8 |
#3: Chemical | ChemComp-NAD / |
#4: Chemical | ChemComp-PSR / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.81 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium citrate pH 5.5, 15% w/v PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9875 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 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: 2.4→50 Å / Num. obs: 19566 / % possible obs: 99.4 % / Redundancy: 12.1 % / CC1/2: 0.979 / CC star: 0.995 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.051 / Rrim(I) all: 0.18 / Χ2: 0.987 / Net I/σ(I): 6.2 / Num. measured all: 235980 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8JFM Resolution: 2.41→40.29 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.08 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.41→40.29 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|