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Yorodumi- PDB-6okg: Crosslinked Crystal Structure of Type II Fatty Acid Synthase Keto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6okg | |||||||||
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Title | Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabF, and C16-crypto Acyl Carrier Protein, AcpP | |||||||||
Components |
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Keywords | TRANSFERASE / Thiolase / ketosynthase / KS / AcpP | |||||||||
Function / homology | Function and homology information fatty acid elongation, saturated fatty acid / monounsaturated fatty acid biosynthetic process / beta-ketoacyl-[acyl-carrier-protein] synthase II / lipid biosynthetic process / lipid A biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / acyl binding / acyl carrier activity / response to cold ...fatty acid elongation, saturated fatty acid / monounsaturated fatty acid biosynthetic process / beta-ketoacyl-[acyl-carrier-protein] synthase II / lipid biosynthetic process / lipid A biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / acyl binding / acyl carrier activity / response to cold / fatty acid biosynthetic process / response to xenobiotic stimulus / lipid binding / protein homodimerization activity / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | |||||||||
Authors | Mindrebo, J.T. / Kim, W.E. / Bartholow, T.G. / Chen, A. / Davis, T.D. / La Clair, J. / Burkart, M.D. / Noel, J.P. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2020 Title: Gating mechanism of elongating beta-ketoacyl-ACP synthases. Authors: Mindrebo, J.T. / Patel, A. / Kim, W.E. / Davis, T.D. / Chen, A. / Bartholow, T.G. / La Clair, J.J. / McCammon, J.A. / Noel, J.P. / Burkart, M.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6okg.cif.gz | 202.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6okg.ent.gz | 159.2 KB | Display | PDB format |
PDBx/mmJSON format | 6okg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6okg_validation.pdf.gz | 326.8 KB | Display | wwPDB validaton report |
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Full document | 6okg_full_validation.pdf.gz | 328.5 KB | Display | |
Data in XML | 6okg_validation.xml.gz | 1.8 KB | Display | |
Data in CIF | 6okg_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/6okg ftp://data.pdbj.org/pub/pdb/validation_reports/ok/6okg | HTTPS FTP |
-Related structure data
Related structure data | 6okcC 6okfC 6oltC 2facS 2gfwS S: Starting model for refinement C: citing same article (ref.) |
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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: 43089.629 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: fabF, fabJ, b1095, JW1081 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P0AAI5, beta-ketoacyl-[acyl-carrier-protein] synthase II |
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#2: Protein | Mass: 8645.460 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: acpP, b1094, JW1080 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A6A8 |
#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-MU4 / |
#5: 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: 2.07 Å3/Da / Density % sol: 40.71 % / Description: Orange Rods |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30 % PEG 8K, 0.1 M sodium cacodylate pH 6.5, and 0.3 M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å | |||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 14, 2017 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.3→86.89 Å / Num. obs: 20047 / % possible obs: 100 % / Redundancy: 19.1 % / Biso Wilson estimate: 27.25 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.368 / Rpim(I) all: 0.085 / Rrim(I) all: 0.378 / Net I/σ(I): 9.2 / Num. measured all: 382501 / Scaling rejects: 2023 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GFW was used as the search model for FabF, 2FAC was used as the search model for AcpP Resolution: 2.3→69.045 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.37 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 135.73 Å2 / Biso mean: 31.8894 Å2 / Biso min: 14.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→69.045 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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