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Yorodumi- PDB-3il6: Structure of E. faecalis FabH in complex with 2-({4-[(3R,5S)-3,5-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3il6 | ||||||
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Title | Structure of E. faecalis FabH in complex with 2-({4-[(3R,5S)-3,5-dimethylpiperidin-1-yl]-3-phenoxybenzoyl}amino)benzoic acid | ||||||
Components | 3-oxoacyl-[acyl-carrier-protein] synthase 3 | ||||||
Keywords | TRANSFERASE / FabH / fatty acid biosynthesis / antibiotic / Acyltransferase / Cytoplasm / Lipid synthesis / Multifunctional enzyme | ||||||
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 biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Gajiwala, K.S. / Margosiak, S. / Lu, J. / Cortez, J. / Su, Y. / Nie, Z. / Appelt, K. | ||||||
Citation | Journal: Febs Lett. / Year: 2009 Title: Crystal structures of bacterial FabH suggest a molecular basis for the substrate specificity of the enzyme. Authors: Gajiwala, K.S. / Margosiak, S. / Lu, J. / Cortez, J. / Su, Y. / Nie, Z. / Appelt, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3il6.cif.gz | 81.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3il6.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 3il6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/il/3il6 ftp://data.pdbj.org/pub/pdb/validation_reports/il/3il6 | HTTPS FTP |
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-Related structure data
Related structure data | 3il3C 3il4C 3il5SC 3il7C 3il9C C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 35185.875 Da / Num. of mol.: 1 / Mutation: D36A, E37A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: EF_2885, fabH / Production host: Escherichia coli (E. coli) References: UniProt: Q820T1, beta-ketoacyl-[acyl-carrier-protein] synthase III | ||
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#2: Chemical | ChemComp-B83 / | ||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.02 Å3/Da / Density % sol: 69.41 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2004 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→25 Å / Num. all: 20488 / Num. obs: 19811 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Biso Wilson estimate: 39.7 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 4.33 / Num. unique all: 1939 / Rsym value: 0.361 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IL5 Resolution: 2.5→24.36 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 519487.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.9522 Å2 / ksol: 0.355255 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→24.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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