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- PDB-6t62: Crystal structure of Acinetobacter baumannii FabG in complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6t62 | ||||||
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Title | Crystal structure of Acinetobacter baumannii FabG in complex with NADPH at 1.8 A resolution | ||||||
![]() | 3-oxoacyl-(Acyl-carrier-protein) reductase | ||||||
![]() | BIOSYNTHETIC PROTEIN / Fatty acid biosynthesis / FabG / (3-oxoacyl-(Acyl-carrier-protein) reductase) / NADP / NADPH / complex / FAS-II | ||||||
Function / homology | ![]() 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid biosynthetic process / NAD binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vella, P. / Schnell, R. / Schneider, G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A FabG inhibitor targeting an allosteric binding site inhibits several orthologs from Gram-negative ESKAPE pathogens. Authors: Vella, P. / Rudraraju, R.S. / Lundback, T. / Axelsson, H. / Almqvist, H. / Vallin, M. / Schneider, G. / Schnell, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111.2 KB | Display | ![]() |
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PDB format | ![]() | 86.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 22.9 KB | Display | |
Data in CIF | ![]() | 33.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6t5xC ![]() 6t60C ![]() 6t65C ![]() 6t6nC ![]() 6t6pC ![]() 6t77C ![]() 6t7mC ![]() 4afnS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26096.635 Da / Num. of mol.: 2 / Mutation: T2A Source method: isolated from a genetically manipulated source Details: The second amino acid is mutated to Alanine for cloning reason. The database entry of the protein contains Thr (theronine) in positon 2. Source: (gene. exp.) ![]() Gene: fabG_9, fabG, fabG_10, fabG_11, fabG_12, fabG_2, fabG_3, fabG_5, fabG_7, fabG_8, A7M79_02495, A7M90_13795, A7N09_01015, AB719_00430, ABUW_3108, B4R90_07750, B9X91_07565, B9X95_05710, BGC29_ ...Gene: fabG_9, fabG, fabG_10, fabG_11, fabG_12, fabG_2, fabG_3, fabG_5, fabG_7, fabG_8, A7M79_02495, A7M90_13795, A7N09_01015, AB719_00430, ABUW_3108, B4R90_07750, B9X91_07565, B9X95_05710, BGC29_09155, BWP00_12180, C2U32_18365, C3415_14660, CBE85_08910, CBI29_00841, CEJ63_15165, CHQ89_11440, CPI82_11015, CSB70_0489, CYQ93_20585, CYQ93_22950, D9Y30_09730, DCD77_08675, DGS69_00745, DOL94_00645, DVA79_16530, DWA21_01645, E4664_12920, E5D09_05595, EA682_12370, EA685_06995, EGM95_16765, EHF38_14445, EJB02_04655, EKS29_20225, EWO92_12305, EWO96_16390, EWP49_14850, FDF20_02980, LV38_02926, NCTC13305_01645, NT90_07375, SAMEA104305229_02428, SAMEA104305242_00720, SAMEA104305268_02089, SAMEA104305283_02395, SAMEA104305292_02313, SAMEA104305318_02347, SAMEA104305320_01823, SAMEA104305325_02271, SAMEA104305337_03003, SAMEA104305351_01934 Production host: ![]() ![]() References: UniProt: V5VHN7, 3-oxoacyl-[acyl-carrier-protein] reductase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.88 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.1M DL-Malic acid pH7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→43.82 Å / Num. obs: 51520 / % possible obs: 93.7 % / Observed criterion σ(I): 2.2 / Redundancy: 8 % / Biso Wilson estimate: 24.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.034 / Rrim(I) all: 0.071 / Rsym value: 0.063 / Net I/av σ(I): 18.6 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3200 / CC1/2: 0.684 / Rpim(I) all: 0.498 / % possible all: 95.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4AFN Resolution: 1.8→43.82 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.066 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.101 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 83.92 Å2 / Biso mean: 28.628 Å2 / Biso min: 14.08 Å2
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Refinement step | Cycle: final / Resolution: 1.8→43.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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