+Open data
-Basic information
Entry | Database: PDB / ID: 5i7n | |||||||||
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Title | MaoC-like dehydratase | |||||||||
Components | MaoC-like dehydratase | |||||||||
Keywords | LYASE / enzyme / hydratase / MaoC like | |||||||||
Function / homology | N-terminal of MaoC-like dehydratase / N-terminal half of MaoC dehydratase / MaoC-like dehydratase domain / MaoC like domain / HotDog domain superfamily / fatty acid metabolic process / MaoC-like dehydratase Function and homology information | |||||||||
Biological species | Mycobacterium abscessus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | |||||||||
Authors | Blaise, M. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Deletion of a dehydratase important for intracellular growth and cording renders rough Mycobacterium abscessus avirulent. Authors: Halloum, I. / Carrere-Kremer, S. / Blaise, M. / Viljoen, A. / Bernut, A. / Le Moigne, V. / Vilcheze, C. / Guerardel, Y. / Lutfalla, G. / Herrmann, J.L. / Jacobs, W.R. / Kremer, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5i7n.cif.gz | 154.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i7n.ent.gz | 120.6 KB | Display | PDB format |
PDBx/mmJSON format | 5i7n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/5i7n ftp://data.pdbj.org/pub/pdb/validation_reports/i7/5i7n | HTTPS FTP |
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-Related structure data
Related structure data | 4v12S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 36672.246 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Gene: MAB_4780 / Plasmid: pET-32 ek/lic / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): rosetta 2 pLys / References: UniProt: B1MM63 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.21 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris-HCl pH8.5, 2.8 M AmSO4, 1mM trans-2-dodecanoyl-CoA |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 52624 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.65→1.69 Å / Redundancy: 6.58 % / Mean I/σ(I) obs: 2.12 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4v12 Resolution: 1.65→42.772 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.71
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→42.772 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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