+Open data
-Basic information
Entry | Database: PDB / ID: 3il9 | ||||||
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Title | Structure of E. coli FabH | ||||||
Components | 3-oxoacyl-[acyl-carrier-protein] synthase 3 | ||||||
Keywords | TRANSFERASE / FabH / fatty acid biosynthesis / antibiotic / Acyltransferase / 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 metabolic process / fatty acid biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 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 | 3il9.cif.gz | 136.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3il9.ent.gz | 105.7 KB | Display | PDB format |
PDBx/mmJSON format | 3il9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3il9_validation.pdf.gz | 434.6 KB | Display | wwPDB validaton report |
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Full document | 3il9_full_validation.pdf.gz | 438.4 KB | Display | |
Data in XML | 3il9_validation.xml.gz | 27 KB | Display | |
Data in CIF | 3il9_validation.cif.gz | 39 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/il/3il9 ftp://data.pdbj.org/pub/pdb/validation_reports/il/3il9 | HTTPS FTP |
-Related structure data
Related structure data | 3il3C 3il4C 3il5C 3il6C 3il7C 1eblS 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: 36358.926 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: b1091, fabH, JW1077 / Production host: Escherichia coli (E. coli) References: UniProt: P0A6R0, beta-ketoacyl-[acyl-carrier-protein] synthase III #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.3 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 12% PEG 3350, 5 mM calcium acetate, 0.1 M HEPES, pH 7.5, 2 mM TCEP and 1% DMSO, 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: 1.85→25 Å / Num. all: 59836 / Num. obs: 58098 / % possible obs: 97.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 21 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 4 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.446 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EBL Resolution: 1.85→24.97 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 371464.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.2349 Å2 / ksol: 0.372154 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→24.97 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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