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Yorodumi- PDB-4oxy: Substrate-binding loop movement with inhibitor PT10 in the tetram... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oxy | ||||||||||||
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Title | Substrate-binding loop movement with inhibitor PT10 in the tetrameric Mycobacterium tuberculosis enoyl-ACP reductase InhA | ||||||||||||
Components | Enoyl-[acyl-carrier-protein] reductase [NADH] | ||||||||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Bacterial fatty acid biosynthesis / enzyme-inhibitor complex / substrate-binding loop refolding / conformational heterogeneity / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||||||||
Function / homology | Function and homology information enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD+ binding / peptidoglycan-based cell wall / fatty acid binding / fatty acid biosynthetic process ...enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD+ binding / peptidoglycan-based cell wall / fatty acid binding / fatty acid biosynthetic process / response to antibiotic / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3501 Å | ||||||||||||
Authors | Li, H.J. / Sullivan, T.J. / Pan, P. / Lai, C.T. / Liu, N. / Garcia-Diaz, M. / Simmerling, C. / Tonge, P.J. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Acs Chem.Biol. / Year: 2014 Title: A Structural and Energetic Model for the Slow-Onset Inhibition of the Mycobacterium tuberculosis Enoyl-ACP Reductase InhA. Authors: Li, H.J. / Lai, C.T. / Pan, P. / Yu, W. / Liu, N. / Bommineni, G.R. / Garcia-Diaz, M. / Simmerling, C. / Tonge, P.J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oxy.cif.gz | 414.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oxy.ent.gz | 338.3 KB | Display | PDB format |
PDBx/mmJSON format | 4oxy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/4oxy ftp://data.pdbj.org/pub/pdb/validation_reports/ox/4oxy | HTTPS FTP |
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-Related structure data
Related structure data | 4ohuC 4oxkC 4oxnC 4oyrC 2x23S C: citing same article (ref.) 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
#1: Protein | Mass: 30726.131 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC BAA-935 / AF2122/97 / Gene: MT1531,MTCY277.05,Rv1484,inhA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: P0A5Y6, UniProt: P9WGR1*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH) #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-1TN / #4: 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: 2.65 Å3/Da / Density % sol: 53.57 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 250 mM ammonium acetate, 14% PEG 4000, 6% DMSO |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 6, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.35→50 Å / Num. obs: 51056 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 33.95 Å2 / Rmerge(I) obs: 0.08 / Χ2: 0.876 / Net I/av σ(I): 22.436 / Net I/σ(I): 11 / Num. measured all: 365630 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2X23 Resolution: 2.3501→43.547 Å / FOM work R set: 0.8665 / SU ML: 0.74 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.27 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.084 Å2 / ksol: 0.349 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.39 Å2 / Biso mean: 34.2 Å2 / Biso min: 12.49 Å2
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Refinement step | Cycle: final / Resolution: 2.3501→43.547 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18
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Refinement TLS params. | Method: refined / Origin x: -19.2196 Å / Origin y: 13.1324 Å / Origin z: 25.5768 Å
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Refinement TLS group |
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