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Yorodumi- PDB-6t60: Crystal structure of Acinetobacter baumannii FabG at 1.66 A resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t60 | ||||||
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Title | Crystal structure of Acinetobacter baumannii FabG at 1.66 A resolution | ||||||
Components | 3-oxoacyl-(Acyl-carrier-protein) reductase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Fatty acid biosynthesis / FabG / (3-oxoacyl-(Acyl-carrier-protein) reductase) / FAS-II | ||||||
Function / homology | Function and homology information 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 | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | ||||||
Authors | Vella, P. / Schnell, R. / Schneider, G. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Bioorg.Med.Chem. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6t60.cif.gz | 112.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t60.ent.gz | 87.6 KB | Display | PDB format |
PDBx/mmJSON format | 6t60.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6t60_validation.pdf.gz | 423.5 KB | Display | wwPDB validaton report |
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Full document | 6t60_full_validation.pdf.gz | 426.2 KB | Display | |
Data in XML | 6t60_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 6t60_validation.cif.gz | 35.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t6/6t60 ftp://data.pdbj.org/pub/pdb/validation_reports/t6/6t60 | HTTPS FTP |
-Related structure data
Related structure data | 6t5xC 6t62C 6t65C 6t6nC 6t6pC 6t77C 6t7mC 4afnS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 26096.635 Da / Num. of mol.: 2 / Mutation: T2A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) 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 Plasmid: pNIC28Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: V5VHN7, 3-oxoacyl-[acyl-carrier-protein] reductase #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: 2.85 Å3/Da / Density % sol: 56.84 % / Description: rod |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979337 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 3, 2014 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979337 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→57.45 Å / Num. obs: 69132 / % possible obs: 98.2 % / Observed criterion σ(I): 1.8 / Redundancy: 6.8 % / Biso Wilson estimate: 17.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.031 / Rrim(I) all: 0.093 / Rsym value: 0.087 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.66→1.75 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 10042 / CC1/2: 0.818 / Rpim(I) all: 0.252 / Rrim(I) all: 0.737 / Rsym value: 0.688 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4AFN Resolution: 1.66→57.45 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.536 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.077 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: 101.41 Å2 / Biso mean: 26.5 Å2 / Biso min: 13.58 Å2
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Refinement step | Cycle: final / Resolution: 1.66→57.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.66→1.703 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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