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Yorodumi- PDB-4b0b: Crystal Structure of 3-hydroxydecanoyl-Acyl Carrier Protein Dehyd... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b0b | ||||||
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Title | Crystal Structure of 3-hydroxydecanoyl-Acyl Carrier Protein Dehydratase (FabA) from Pseudomonas aeruginosa in complex with 3-(pyridin-2-yloxy)aniline | ||||||
Components | 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE | ||||||
Keywords | LYASE / FATTY ACID BIOSYNTHESIS / BACTERIAL VIRULENCE / DRUG DISCOVERY | ||||||
Function / homology | Function and homology information 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 | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Moynie, L. / McMahon, S.A. / Duthie, F.G. / Taylor, J.W. / Naismith, J.H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2013 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b0b.cif.gz | 156.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b0b.ent.gz | 124.5 KB | Display | PDB format |
PDBx/mmJSON format | 4b0b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4b0b_validation.pdf.gz | 448.2 KB | Display | wwPDB validaton report |
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Full document | 4b0b_full_validation.pdf.gz | 450.5 KB | Display | |
Data in XML | 4b0b_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 4b0b_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/4b0b ftp://data.pdbj.org/pub/pdb/validation_reports/b0/4b0b | HTTPS FTP |
-Related structure data
Related structure data | 4b0cC 4b0iC 4b0jC 4b8uC 4fq9SC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (-0.9995, -0.03104, 0.002804), Vector: |
-Components
#1: Protein | Mass: 18768.533 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PA01 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): TUNER / References: UniProt: O33877, EC: 4.2.1.60 #2: Chemical | #3: 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: 2.3 Å3/Da / Density % sol: 49.6 % / Description: NONE |
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Crystal grow | pH: 8 Details: 15 % PEG 8000,0.2 M MAGNESIUM CHLORIDE, TRIS-HCL PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX / Wavelength: 1.54178 |
Detector | Type: RIGAKU CCD / Detector: CCD / Date: Feb 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→37.3 Å / Num. obs: 26978 / % possible obs: 99 % / Observed criterion σ(I): -3.7 / Redundancy: 7.78 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.9→1.92 Å / Redundancy: 4.43 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.21 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4FQ9 Resolution: 1.9→37.3 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.94 / SU B: 8.29 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.155 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.927 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→37.3 Å
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Refine LS restraints |
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