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Yorodumi- PDB-5buy: Crystal Structure of beta-hydroxyacyl-acyl carrier protein dehydr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5buy | ||||||
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Title | Crystal Structure of beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ) from Francisella tularensis | ||||||
Components | 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ | ||||||
Keywords | LYASE / FabZ / antimicrobial target / fatty acid synthesis / hot-dog fold / trimer of dimers | ||||||
Function / homology | Function and homology information (3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity / (3R)-3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity / (3R)-3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity / lipid A biosynthetic process / fatty acid biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Francisella tularensis subsp. tularensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | McGillick, B. / Kumaran, D. / Swaminathan, S. | ||||||
Citation | Journal: To be published Title: Crystal Structure of beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ) from Francisella tularensis Authors: McGillick, B. / Kumaran, D. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5buy.cif.gz | 175.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5buy.ent.gz | 139.1 KB | Display | PDB format |
PDBx/mmJSON format | 5buy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/5buy ftp://data.pdbj.org/pub/pdb/validation_reports/bu/5buy | HTTPS FTP |
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-Related structure data
Related structure data | 1zhgS 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: 19843.064 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4) (bacteria) Strain: SCHU S4 / Schu 4 / Gene: fabZ, FTT_1570c / Plasmid: pET28B / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q5NEQ0, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5, 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.07 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→50 Å / Num. all: 31876 / Num. obs: 31876 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 2.55→2.64 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 1.5 / % possible all: 90.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1ZHG Resolution: 2.55→45.22 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.892 / SU B: 11.427 / SU ML: 0.255 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.7 / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.001 Å2
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Refinement step | Cycle: 1 / Resolution: 2.55→45.22 Å
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Refine LS restraints |
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