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- PDB-4b8u: Crystal Structure of 3-hydroxydecanoyl-Acyl Carrier Protein Dehyd... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4b8u | ||||||
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Title | Crystal Structure of 3-hydroxydecanoyl-Acyl Carrier Protein Dehydratase (FabA) from Pseudomonas aeruginosa in complex with N- isobutyl-2-(5-(2-thienyl)-1,2-oxazol-3-yl-)methoxy)acetamide | ||||||
![]() | 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE | ||||||
![]() | LYASE / FATTY ACID BIOSYNTHESIS / INHIBITOR / BACTERIAL VIRULENCE / DRUG DISCOVERY | ||||||
Function / homology | ![]() trans-2-decenoyl-[acyl-carrier protein] isomerase / trans-2-decenoyl-acyl-carrier-protein isomerase activity / unsaturated fatty acid biosynthetic process / : / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Moynie, L. / McMahon, S.A. / Duthie, F.G. / Brenk, R. / Naismith, J.H. | ||||||
![]() | ![]() Title: Structural Insights Into the Mechanism and Inhibition of the Beta-Hydroxydecanoyl-Acyl Carrier Protein Dehydratase from Pseudomonasaeruginosa. Authors: Moynie, L. / Leckie, S.M. / Mcmahon, S.A. / Duthie, F.G. / Koehnke, A. / Taylor, J.W. / Alphey, M.S. / Brenk, R. / Smith, A.D. / Naismith, J.H. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 332.2 KB | Display | ![]() |
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PDB format | ![]() | 275.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 751.5 KB | Display | ![]() |
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Full document | ![]() | 756.8 KB | Display | |
Data in XML | ![]() | 29.8 KB | Display | |
Data in CIF | ![]() | 41 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4b0bC ![]() 4b0cC ![]() 4b0iC ![]() 4b0jC ![]() 4fq9SC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18768.533 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-IBK / | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 60 % / Description: NONE |
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Crystal grow | pH: 5 Details: PEG MME 5000 13 %, 100 MM SODIUM CITRATE PH 5.0, LITHIUM SULPHATE 0.1 M |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 6, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.78→71.83 Å / Num. obs: 27828 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.76→2.83 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4FQ9 Resolution: 2.76→71.83 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / SU B: 25.72 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 1.866 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.659 Å2
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Refinement step | Cycle: LAST / Resolution: 2.76→71.83 Å
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Refine LS restraints |
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