[English] 日本語
Yorodumi- PDB-4afn: Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4afn | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase (FabG) from Pseudomonas aeruginosa at 2.3A resolution | ||||||
Components | 3-OXOACYL-[ACYL-CARRIER-PROTEIN] REDUCTASE FABG | ||||||
Keywords | OXIDOREDUCTASE / FATTY ACID BIOSYNTHESIS / ROSSMANN FOLD | ||||||
Function / homology | Function and homology information 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid elongation / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / NADP binding Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Cukier, C.D. / Schnell, R. / Schneider, G. / Lindqvist, Y. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2013 Title: Discovery of an Allosteric Inhibitor Binding Site in 3-Oxo-Acyl-Acp Reductase from Pseudomonas Aeruginosa Authors: Cukier, C.D. / Hope, A. / Elamin, A. / Moynie, L. / Schnell, R. / Schach, S. / Kneuper, H. / Singh, M. / Naismith, J. / Lindqvist, Y. / Gray, D. / Schneider, G. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2013 Title: The Aeropath Project Targeting Pseudomonas Aeruginosa: Crystallographic Studies for Assessment of Potential Targets in Early-Stage Drug Discovery. Authors: Moynie, L. / Schnell, R. / Mcmahon, S.A. / Sandalova, T. / Boulkerou, W.A. / Schmidberger, J.W. / Alphey, M. / Cukier, C. / Duthie, F. / Kopec, J. / Liu, H. / Jacewicz, A. / Hunter, W.N. / ...Authors: Moynie, L. / Schnell, R. / Mcmahon, S.A. / Sandalova, T. / Boulkerou, W.A. / Schmidberger, J.W. / Alphey, M. / Cukier, C. / Duthie, F. / Kopec, J. / Liu, H. / Jacewicz, A. / Hunter, W.N. / Naismith, J.H. / Schneider, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4afn.cif.gz | 190.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4afn.ent.gz | 151 KB | Display | PDB format |
PDBx/mmJSON format | 4afn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/4afn ftp://data.pdbj.org/pub/pdb/validation_reports/af/4afn | HTTPS FTP |
---|
-Related structure data
Related structure data | 4ag3C 4bntC 4bnuC 4bnvC 4bnwC 4bnxC 4bnyC 4bnzC 4bo0C 4bo1C 4bo2C 4bo3C 4bo4C 4bo5C 4bo6C 4bo7C 4bo8C 4bo9C 3ftpS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||
Unit cell |
| ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
#1: Protein | Mass: 28167.961 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O54438, 3-oxoacyl-[acyl-carrier-protein] reductase #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.4 % / Description: NONE |
---|---|
Crystal grow | pH: 7.8 Details: 0.1 M TRIS-HCL PH 7.8, 10% (W/V)PEG 3350, PROTEIN CONCENTRATION 8MG/ML |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 4, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→33.16 Å / Num. obs: 45767 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 33.4 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FTP Resolution: 2.3→33.16 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.888 / SU B: 8.378 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.341 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.131 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→33.16 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|