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- PDB-5cg2: Crystal structure of E. coli FabI bound to the thiocarbamoylated ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5cg2 | ||||||
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Title | Crystal structure of E. coli FabI bound to the thiocarbamoylated benzodiazaborine inhibitor 35b. | ||||||
![]() | Enoyl-[acyl-carrier-protein] reductase [NADH] FabI | ||||||
![]() | Oxidoreductase/Oxidoreductase Inhibitor / antibiotics / NAD / enoyl-ACP reductase / Oxidoreducatase-Oxidoreducatase Inhibitor complex / Oxidoreductase-Oxidoreductase Inhibitor complex | ||||||
Function / homology | ![]() enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / NADH binding / biotin biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / lipid biosynthetic process / catalytic complex / protein homotetramerization / response to antibiotic ...enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / NADH binding / biotin biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / lipid biosynthetic process / catalytic complex / protein homotetramerization / response to antibiotic / protein-containing complex / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jordan, C.A. / Vey, J.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystallographic insights into the structure-activity relationships of diazaborine enoyl-ACP reductase inhibitors. Authors: Jordan, C.A. / Sandoval, B.A. / Serobyan, M.V. / Gilling, D.H. / Groziak, M.P. / Xu, H.H. / Vey, J.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112.7 KB | Display | ![]() |
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PDB format | ![]() | 84.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 30.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5cfzSC ![]() 5cg1C 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 2 - 257 / Label seq-ID: 45 - 300
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Components
#1: Protein | Mass: 32691.133 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: fabI, envM, b1288, JW1281 / Plasmid: pET30 / Production host: ![]() ![]() References: UniProt: P0AEK4, enoyl-[acyl-carrier-protein] reductase (NADH) #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.11 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M citrate pH 7.0, 0.1M ammonium sulfate, 22%w/v PEG 2000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.11→69.21 Å / Num. all: 36240 / Num. obs: 36240 / % possible obs: 99.3 % / Redundancy: 17.2 % / Rpim(I) all: 0.012 / Rrim(I) all: 0.049 / Rsym value: 0.048 / Net I/av σ(I): 10.4 / Net I/σ(I): 42.6 / Num. measured all: 624835 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5CFZ Resolution: 2.11→69.21 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.117 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.01 Å2 / Biso mean: 24.417 Å2 / Biso min: 9.99 Å2
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Refinement step | Cycle: final / Resolution: 2.11→69.21 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 308 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.111→2.166 Å / Total num. of bins used: 20
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