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Yorodumi- PDB-4qav: The structure of Beta-ketoacyl -(acyl carrier protein) synthase I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qav | ||||||
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Title | The structure of Beta-ketoacyl -(acyl carrier protein) synthase II (FabF) from Neisseria meningitidis | ||||||
Components | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | ||||||
Keywords | TRANSFERASE / KASII / FabF / CONDENSING ENZYME | ||||||
Function / homology | Function and homology information beta-ketoacyl-[acyl-carrier-protein] synthase II / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process Similarity search - Function | ||||||
Biological species | Neisseria meningitidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Nanson, J.D. / Forwood, J.K. | ||||||
Citation | Journal: to be published Title: The structure of Beta-ketoacyl -(acyl carrier protein) synthase II (FabF) from Neisseria meningitidis Authors: 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 | 4qav.cif.gz | 316.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qav.ent.gz | 262.9 KB | Display | PDB format |
PDBx/mmJSON format | 4qav.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qav_validation.pdf.gz | 438.3 KB | Display | wwPDB validaton report |
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Full document | 4qav_full_validation.pdf.gz | 442.9 KB | Display | |
Data in XML | 4qav_validation.xml.gz | 33.9 KB | Display | |
Data in CIF | 4qav_validation.cif.gz | 49.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/4qav ftp://data.pdbj.org/pub/pdb/validation_reports/qa/4qav | HTTPS FTP |
-Related structure data
Related structure data | 2gfwS 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: 43177.504 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: alpha14 / Gene: fabF / Production host: Escherichia coli (E. coli) References: UniProt: C6S978, beta-ketoacyl-[acyl-carrier-protein] synthase II #2: Chemical | #3: Chemical | #4: 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: 2.62 Å3/Da / Density % sol: 53.01 % |
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Crystal grow | Temperature: 296.15 K / Method: vapor diffusion, hanging drop Details: 20% PEG 3350, 250mM Sodium Formate, VAPOR DIFFUSION, HANGING DROP, temperature 296.15K |
-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: Jul 13, 2013 | |||||||||
Radiation | Monochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | |||||||||
Reflection | Resolution: 2.1→33.23 Å / Num. all: 52300 / Num. obs: 52092 / % possible obs: 99.6 % / Biso Wilson estimate: 24.01 Å2 | |||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GFW Resolution: 2.1→32.24 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 19.06 / 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: 77.35 Å2 / Biso mean: 31.5992 Å2 / Biso min: 13.18 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→32.24 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19
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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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