[English] 日本語
Yorodumi- PDB-2gyo: Methanethiol-Cys 112 Inhibition Complex of E. Coli Ketoacyl Synth... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gyo | ||||||
---|---|---|---|---|---|---|---|
Title | Methanethiol-Cys 112 Inhibition Complex of E. Coli Ketoacyl Synthase III (FabH) and Coenzyme A | ||||||
Components | 3-oxoacyl-[acyl-carrier-protein] synthase 3 | ||||||
Keywords | TRANSFERASE / fatty acid biosynthesis / alkyl-coa-disulfide / mechanism-based inhibitor / mycobacterium tuberculosis | ||||||
Function / homology | Function and homology information beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid metabolic process / fatty acid biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Alhamadsheh, M.M. / Musayev, F. / Komissarov, A.A. / Sachdeva, S. / Wright, H.T. / Scarsdale, N. / Florova, G. / Reynolds, K.A. | ||||||
Citation | Journal: Chem.Biol. / Year: 2007 Title: Alkyl-CoA Disulfides as Inhibitors and Mechanistic Probes for FabH Enzymes. Authors: Alhamadsheh, M.M. / Musayev, F. / Komissarov, A.A. / Sachdeva, S. / Wright, H.T. / Scarsdale, N. / Florova, G. / Reynolds, K.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2gyo.cif.gz | 129 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2gyo.ent.gz | 107.4 KB | Display | PDB format |
PDBx/mmJSON format | 2gyo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gy/2gyo ftp://data.pdbj.org/pub/pdb/validation_reports/gy/2gyo | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The asymmetric unit contains the dimer corresponding to the biological assembly |
-Components
#1: Protein | Mass: 33547.027 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fabH / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3 pLysE)/pLH14 References: UniProt: P0A6R0, beta-ketoacyl-[acyl-carrier-protein] synthase I #2: Chemical | ChemComp-COA / | #3: Chemical | ChemComp-MEE / | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.51 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.7M ammonium sulfate, 2% PEG400, 100 mM Na Hepes (pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 17, 2005 / Details: Rigaku Varimax Confocal Optics |
Radiation | Monochromator: Rigaku Varimax Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→31.09 Å / Num. all: 44165 / Num. obs: 42137 / % possible obs: 95.4 % / Redundancy: 5.09 % / Rsym value: 0.069 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5.41 % / Mean I/σ(I) obs: 5.8 / Rsym value: 0.264 / % possible all: 97.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.91 / SU B: 11.216 / SU ML: 0.153 / TLS residual ADP flag: LIKELY RESIDUAL Isotropic thermal model: TLS groups for each protein chain with residual isotropic B factors for each atom Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.515 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.293 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|