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Open data
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Basic information
Entry | Database: PDB / ID: 6o0n | ||||||
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Title | M.tb MenD with Inhibitor | ||||||
![]() | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | ||||||
![]() | transferase/transferase inhibitor / menaquinone biosynthesis / ThDP dependent / decarboxylation / C-C bond ligation / ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Johnston, J.M. / Ho, N.A.T. / Bashiri, G. / Bulloch, E.M. / Nigon, L.V. / Jirgis, E.M.N. / Baker, E.N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Allosteric regulation of menaquinone (vitamin K2) biosynthesis in the human pathogenMycobacterium tuberculosis. Authors: Bashiri, G. / Nigon, L.V. / Jirgis, E.N.M. / Ho, N.A.T. / Stanborough, T. / Dawes, S.S. / Baker, E.N. / Bulloch, E.M.M. / Johnston, J.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 373.9 KB | Display | ![]() |
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PDB format | ![]() | 298.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6o04C ![]() 6o0gC ![]() 6o0jC ![]() 5eryS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 60068.945 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 25618 / H37Rv / Gene: menD, Rv0555 Production host: ![]() References: UniProt: P9WK11, ![]() #2: Chemical | ChemComp-DNA / #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.66 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Morpheus condition. MOPS/HEPES pH 7.5, PEG 4K, CA mix, glycerol |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2016 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||
Reflection | Resolution: 3.03→48.12 Å / Num. obs: 53451 / % possible obs: 100 % / Redundancy: 14.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.316 / Rpim(I) all: 0.084 / Rrim(I) all: 0.327 / Net I/σ(I): 10 / Num. measured all: 797300 / Scaling rejects: 2 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5ERY Resolution: 3.03→48.119 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.99
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 142.77 Å2 / Biso mean: 78.7046 Å2 / Biso min: 38.7 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.03→48.119 Å
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