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Yorodumi- PDB-5sxo: 1.35 angstrom resolution crystal structure of beta-ketoacyl-ACP s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5sxo | ||||||
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Title | 1.35 angstrom resolution crystal structure of beta-ketoacyl-ACP synthase II (FabF) from Listeria monocytogenes | ||||||
Components | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | ||||||
Keywords | TRANSFERASE / KASII / FABF / CONDENSING ENZYME | ||||||
Function / homology | Function and homology information 3-oxoacyl-[acyl-carrier-protein] synthase activity => GO:0004315 / beta-ketoacyl-[acyl-carrier-protein] synthase II / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process Similarity search - Function | ||||||
Biological species | Listeria monocytogenes ATCC 19115 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Soares da Costa, T.P. / Nanson, J.D. / Forwood, J.K. | ||||||
Citation | Journal: To Be Published Title: 1.35 angstrom resolution crystal structure of beta-ketoacyl-ACP synthase II (FabF) from Listeria monocytogenes Authors: Soares da Costa, T.P. / Nanson, J.D. / Forwood, J.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5sxo.cif.gz | 246.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5sxo.ent.gz | 200.3 KB | Display | PDB format |
PDBx/mmJSON format | 5sxo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sx/5sxo ftp://data.pdbj.org/pub/pdb/validation_reports/sx/5sxo | HTTPS FTP |
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-Related structure data
Related structure data | 3o04S 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: 44331.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes ATCC 19115 (bacteria) Gene: LmNIHS28_01559, M643_06390 / Production host: Escherichia coli (E. coli) References: UniProt: A0A0B8RFI6, beta-ketoacyl-[acyl-carrier-protein] synthase II |
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#2: 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: 2.61 Å3/Da / Density % sol: 52.9 % |
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Crystal grow | Temperature: 296.15 K / Method: vapor diffusion, hanging drop Details: 0.2 M potassium sodium tartrate tetrahydrate, 0.1 M sodium citrate tribasic dihydrate pH 5.6, 2 M ammonium sulphate, 22.5% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→28.52 Å / Num. obs: 103454 / % possible obs: 99.7 % / Redundancy: 4.8 % / CC1/2: 0.997 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3O04 Resolution: 1.35→28.517 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.29
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→28.517 Å
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Refine LS restraints |
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LS refinement shell |
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