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Yorodumi- PDB-4nqz: Crystal Structure of the Pseudomonas aeruginosa Enoyl-Acyl Carrie... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nqz | ||||||
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Title | Crystal Structure of the Pseudomonas aeruginosa Enoyl-Acyl Carrier Protein Reductase (FabI) in apo form | ||||||
Components | Enoyl-[acyl-carrier-protein] reductase [NADH] FabI | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold motif / reductase / cytosol | ||||||
Function / homology | Function and homology information enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / identical protein binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.604 Å | ||||||
Authors | Chi, Y.M. / Lee, J.H. / Park, A.K. | ||||||
Citation | Journal: Bull.Korean Chem.Soc. / Year: 2015 Title: Crystal Structures of Pseudomonas aeruginosa Enoyl-ACP Reductase (FabI) in the Presence and Absence of NAD+ and Triclosan Authors: Lee, J.H. / Park, A.K. / Chi, Y.M. / Jeong, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nqz.cif.gz | 707.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nqz.ent.gz | 586.7 KB | Display | PDB format |
PDBx/mmJSON format | 4nqz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nqz_validation.pdf.gz | 575.6 KB | Display | wwPDB validaton report |
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Full document | 4nqz_full_validation.pdf.gz | 648 KB | Display | |
Data in XML | 4nqz_validation.xml.gz | 134.9 KB | Display | |
Data in CIF | 4nqz_validation.cif.gz | 188.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/4nqz ftp://data.pdbj.org/pub/pdb/validation_reports/nq/4nqz | HTTPS FTP |
-Related structure data
Related structure data | 4nr0C 1c14S 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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-Components
#1: Protein | Mass: 29106.936 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: fabI, PA1806 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9ZFE4, enoyl-[acyl-carrier-protein] reductase (NADH) #2: 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: 2.37 Å3/Da / Density % sol: 48.13 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 6% tacsimate, 8% PEG 3350, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 10, 2009 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 132518 / Num. obs: 112296 / % possible obs: 84.74 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 37.74 Å2 |
Reflection shell | Resolution: 2.6→2.64 Å / % possible all: 67.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1c14 Resolution: 2.604→44.394 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7723 / SU ML: 0.56 / σ(F): 1.48 / Phase error: 31.71 / 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: 109.83 Å2 / Biso mean: 40.21 Å2 / Biso min: 12.27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.604→44.394 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: 30
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