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Yorodumi- PDB-3il5: Structure of E. faecalis FabH in complex with 2-({4-bromo-3-[(die... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3il5 | ||||||
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Title | Structure of E. faecalis FabH in complex with 2-({4-bromo-3-[(diethylamino)sulfonyl]benzoyl}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: 2.6 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 | 3il5.cif.gz | 254.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3il5.ent.gz | 206.9 KB | Display | PDB format |
PDBx/mmJSON format | 3il5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3il5_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 3il5_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 3il5_validation.xml.gz | 52 KB | Display | |
Data in CIF | 3il5_validation.cif.gz | 69.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/il/3il5 ftp://data.pdbj.org/pub/pdb/validation_reports/il/3il5 | HTTPS FTP |
-Related structure data
Related structure data | 3il3C 3il4C 3il6C 3il7C 3il9SC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 37663.496 Da / Num. of mol.: 4 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 #2: Chemical | ChemComp-B82 / #3: 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: 2.12 Å3/Da / Density % sol: 42.1 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M lithium sulfate, 0.1 M Bis-Tris, pH 6.5, 25% PEG3350, 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: 2.6→25 Å / Num. all: 38916 / Num. obs: 38358 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3767 / Rsym value: 0.338 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IL9 Resolution: 2.6→25 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 123.34 Å2 / Biso mean: 43.762 Å2 / Biso min: 12.37 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.39 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.016
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