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Yorodumi- PDB-5du6: Crystal structure of M. tuberculosis EchA6 bound to ligand GSK059A. -
+Open data
-Basic information
Entry | Database: PDB / ID: 5du6 | ||||||
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Title | Crystal structure of M. tuberculosis EchA6 bound to ligand GSK059A. | ||||||
Components | Probable enoyl-CoA hydratase echA6 | ||||||
Keywords | LYASE / enoyl-CoA hydratase-like | ||||||
Function / homology | Function and homology information enoyl-CoA hydratase / enoyl-CoA hydratase activity / fatty acid beta-oxidation / peptidoglycan-based cell wall / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å | ||||||
Authors | Cox, J.A.G. / Besra, G.S. / Futterer, K. | ||||||
Citation | Journal: Nat Microbiol / Year: 2016 Title: THPP target assignment reveals EchA6 as an essential fatty acid shuttle in mycobacteria. Authors: Cox, J.A. / Abrahams, K.A. / Alemparte, C. / Ghidelli-Disse, S. / Rullas, J. / Angulo-Barturen, I. / Singh, A. / Gurcha, S.S. / Nataraj, V. / Bethell, S. / Remuinan, M.J. / Encinas, L. / ...Authors: Cox, J.A. / Abrahams, K.A. / Alemparte, C. / Ghidelli-Disse, S. / Rullas, J. / Angulo-Barturen, I. / Singh, A. / Gurcha, S.S. / Nataraj, V. / Bethell, S. / Remuinan, M.J. / Encinas, L. / Jervis, P.J. / Cammack, N.C. / Bhatt, A. / Kruse, U. / Bantscheff, M. / Futterer, K. / Barros, D. / Ballell, L. / Drewes, G. / Besra, G.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5du6.cif.gz | 282.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5du6.ent.gz | 230.9 KB | Display | PDB format |
PDBx/mmJSON format | 5du6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/5du6 ftp://data.pdbj.org/pub/pdb/validation_reports/du/5du6 | HTTPS FTP |
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-Related structure data
Related structure data | 5dtpC 5dtwC 5du4C 5du8C 5ducC 5dufC 3he2S 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: 28230.186 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: echA6, Rv0905, MTCY31.33 / Plasmid: pET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WNP1, enoyl-CoA hydratase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.55 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.6 M tri-sodium citrate, cryoprotected by adding 10 % glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.61→85.9 Å / Num. all: 135533 / Num. obs: 31967 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/av σ(I): 8.7 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.61→2.68 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 2 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HE2 Resolution: 2.61→85.9 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 0.6 / Phase error: 22.97 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.24 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.398 Å2 / ksol: 0.341 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.61→85.9 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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