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Yorodumi- PDB-6ah9: Crystal structure of enoyl-ACP reductase from Acinetobacter bauma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ah9 | ||||||
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Title | Crystal structure of enoyl-ACP reductase from Acinetobacter baumannii in complex with NAD and Triclosan | ||||||
Components | Enoyl-[acyl-carrier-protein] reductase [NADH] | ||||||
Keywords | OXIDOREDUCTASE / Fabi / Acinetobacter baumannii / NAD / Triclosan / Inhibitor complex | ||||||
Function / homology | Function and homology information enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Rani, S.T. / Nataraj, V. / Laxminarasimhan, A. / Thomas, A. / Krishnamurthy, N. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of enoyl-ACP reductase from Acinetobacter baumannii in complex with NAD and Triclosan Authors: Rani, S.T. / Nataraj, V. / Laxminarasimhan, A. / Thomas, A. / Krishnamurthy, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ah9.cif.gz | 68.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ah9.ent.gz | 48.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ah9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/6ah9 ftp://data.pdbj.org/pub/pdb/validation_reports/ah/6ah9 | HTTPS FTP |
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-Related structure data
Related structure data | 4zjuS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 28660.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria) Strain: ATCC 19606 / AUCC 669 / Gene: NC_009085.1 / Plasmid: pET 28a-AbFabI / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A2J1CZK4, UniProt: D0CAD5*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH) |
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#2: Chemical | ChemComp-NAD / |
#3: Chemical | ChemComp-TCL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.5 / Details: 0.1M MES pH 5.5, 100mM NaCl, 10% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2018 |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→72.6 Å / Num. obs: 26533 / % possible obs: 99.7 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.74→1.77 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 4 / Num. unique obs: 1390 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZJU Resolution: 1.74→57.23 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.932 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.127 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.352 Å2
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Refinement step | Cycle: 1 / Resolution: 1.74→57.23 Å
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Refine LS restraints |
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