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Yorodumi- PDB-7umx: Crystal structure of Acinetobacter baumannii FabI in complex with... -
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-Basic information
Entry | Database: PDB / ID: 7umx | ||||||
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Title | Crystal structure of Acinetobacter baumannii FabI in complex with NAD and (R,E)-3-(7-amino-8-oxo-6,7,8,9-tetrahydro-5H-pyrido[2,3-b]azepin-3-yl)-N-methyl-N-((3-methylbenzofuran-2-yl)methyl)acrylamide | ||||||
Components | Enoyl-[acyl-carrier-protein] reductase [NADH] | ||||||
Keywords | ANTIBIOTIC / enoyl reductase / FabI / antimicrobial resistance | ||||||
Function / homology | Function and homology information enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / nucleotide binding Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å | ||||||
Authors | Hajian, B. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Cent.Sci. / Year: 2022 Title: An Iterative Approach Guides Discovery of the FabI Inhibitor Fabimycin, a Late-Stage Antibiotic Candidate with In Vivo Efficacy against Drug-Resistant Gram-Negative Infections Authors: Parker, E.N. / Cain, B.N. / Hajian, B. / Ulrich, R.J. / Geddes, E.J. / Barkho, S. / Lee, H.Y. / Williams, J.D. / Raynor, M. / Caridha, D. / Zaino, A. / Rohde, J.M. / Zak, M. / Shekhar, M. / ...Authors: Parker, E.N. / Cain, B.N. / Hajian, B. / Ulrich, R.J. / Geddes, E.J. / Barkho, S. / Lee, H.Y. / Williams, J.D. / Raynor, M. / Caridha, D. / Zaino, A. / Rohde, J.M. / Zak, M. / Shekhar, M. / Munoz, K.A. / Rzasa, K.M. / Temple, E.R. / Hunt, D. / Jin, X. / Vuong, C. / Pannone, K. / Kelly, A.M. / Mulligan, M.P. / Lee, K.K. / Lau, G.W. / Hung, D.T. / Hergenrother, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7umx.cif.gz | 717 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7umx.ent.gz | 494.8 KB | Display | PDB format |
PDBx/mmJSON format | 7umx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7umx_validation.pdf.gz | 3.8 MB | Display | wwPDB validaton report |
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Full document | 7umx_full_validation.pdf.gz | 3.9 MB | Display | |
Data in XML | 7umx_validation.xml.gz | 70.3 KB | Display | |
Data in CIF | 7umx_validation.cif.gz | 87.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/7umx ftp://data.pdbj.org/pub/pdb/validation_reports/um/7umx | HTTPS FTP |
-Related structure data
Related structure data | 7um8C 7umwC 7umyC 6aheS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 29028.088 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria) Strain: 19606 / Gene: fabI / Production host: Escherichia coli (E. coli) References: UniProt: D0CAD5, enoyl-[acyl-carrier-protein] reductase (NADH) #2: Chemical | ChemComp-NQF / ( #3: Chemical | ChemComp-NAD / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.45 Å3/Da / Density % sol: 49.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM HEPES pH 6.5-7.5 20% PEG 4K 15%-20% 2-propanolol |
-Data collection
Diffraction | Mean temperature: 193 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 6, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→44.95 Å / Num. obs: 65755 / % possible obs: 98.68 % / Redundancy: 2.5 % / CC1/2: 0.99 / Net I/σ(I): 11.39 |
Reflection shell | Resolution: 2.39→2.47 Å / Num. unique obs: 6497 / CC1/2: 0.83 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6AHE Resolution: 2.39→44.95 Å / Cross valid method: FREE R-VALUE / σ(F): 2.13 / Phase error: 27.3448 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 45.31 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.39→44.95 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 29.2002283689 Å / Origin y: 8.363654185 Å / Origin z: 12.0847402076 Å
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Refinement TLS group | Selection details: all |