+Open data
-Basic information
Entry | Database: PDB / ID: 5du8 | ||||||
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Title | Crystal structure of M. tuberculosis EchA6 bound to GSK572A | ||||||
Components | Probable enoyl-CoA hydratase echA6 | ||||||
Keywords | LIPID BINDING PROTEIN / 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: 2.23 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 | 5du8.cif.gz | 282.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5du8.ent.gz | 229.9 KB | Display | PDB format |
PDBx/mmJSON format | 5du8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5du8_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5du8_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5du8_validation.xml.gz | 28.2 KB | Display | |
Data in CIF | 5du8_validation.cif.gz | 38.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/5du8 ftp://data.pdbj.org/pub/pdb/validation_reports/du/5du8 | HTTPS FTP |
-Related structure data
Related structure data | 5dtpC 5dtwC 5du4C 5du6C 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 4
NCS oper:
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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: 3.02 Å3/Da / Density % sol: 59.23 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M sodium chloride, 0.1 M sodium cacodylate pH 6.5, 2 M ammonium sulfate, cryoprotected adding a 10 % ethylene glycol PH range: 6.5 |
-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: May 19, 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: 2.23→96.1 Å / Num. obs: 50922 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.23→2.29 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 2.9 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HE2 Resolution: 2.23→96.07 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.922 / SU B: 11.655 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 mean: 40.413 Å2
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Refinement step | Cycle: 1 / Resolution: 2.23→96.07 Å
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Refine LS restraints |
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