+Open data
-Basic information
Entry | Database: PDB / ID: 3ho2 | |||||||||
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Title | Structure of E.coli FabF(C163A) in complex with Platencin | |||||||||
Components | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | |||||||||
Keywords | TRANSFERASE / FabF / platensimycin / platencin / ketoacyl synthase / Acyltransferase / Fatty acid biosynthesis / Lipid synthesis | |||||||||
Function / homology | Function and homology information fatty acid elongation, saturated fatty acid / monounsaturated fatty acid biosynthetic process / beta-ketoacyl-[acyl-carrier-protein] synthase II / 3-oxoacyl-[acyl-carrier-protein] synthase activity / response to cold / fatty acid biosynthetic process / protein homodimerization activity / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Soisson, S.M. / Parthasarathy, G. | |||||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2009 Title: Isolation, enzyme-bound structure and antibacterial activity of platencin A1 from Streptomyces platensis. Authors: Singh, S.B. / Ondeyka, J.G. / Herath, K.B. / Zhang, C. / Jayasuriya, H. / Zink, D.L. / Parthasarathy, G. / Becker, J.W. / Wang, J. / Soisson, S.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ho2.cif.gz | 101.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ho2.ent.gz | 75.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ho2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/3ho2 ftp://data.pdbj.org/pub/pdb/validation_reports/ho/3ho2 | HTTPS FTP |
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-Related structure data
Related structure data | 3hnzC 3ho9C 3i8pC 2gfvS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 44605.238 Da / Num. of mol.: 1 / Mutation: C163A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b1095, fabF, fabJ, JW1081 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P0AAI5, beta-ketoacyl-[acyl-carrier-protein] synthase II |
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#2: Chemical | ChemComp-N32 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.88 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→39.04 Å / Num. all: 33760 / Num. obs: 33708 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Biso Wilson estimate: 31.692 Å2 / Rsym value: 0.064 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 4.6 / Num. unique all: 3308 / Rsym value: 0.423 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GFV Resolution: 2→39.04 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 34.91 Å2
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Refinement step | Cycle: LAST / Resolution: 2→39.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.12 Å / Total num. of bins used: 9
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