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- PDB-6hf3: M tuberculosis DprE1 in complex with a covalently bound nitrobenz... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6hf3 | ||||||
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Title | M tuberculosis DprE1 in complex with a covalently bound nitrobenzothiazinone | ||||||
![]() | Decaprenylphosphoryl-beta-D-ribose oxidase | ||||||
![]() | FLAVOPROTEIN / oxidation-reduction process / isomerase / arabinan biosynthetic process | ||||||
Function / homology | ![]() arabinan biosynthetic process / cell wall polysaccharide biosynthetic process / decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase / D-arabinono-1,4-lactone oxidase activity / capsule polysaccharide biosynthetic process / FAD binding / cell wall organization / periplasmic space / oxidoreductase activity / response to antibiotic / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Futterer, K. / Batt, S.M. / Besra, G.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Novel insight into the reaction of nitro, nitroso and hydroxylamino benzothiazinones and of benzoxacinones with Mycobacterium tuberculosis DprE1. Authors: Richter, A. / Rudolph, I. / Mollmann, U. / Voigt, K. / Chung, C.W. / Singh, O.M.P. / Rees, M. / Mendoza-Losana, A. / Bates, R. / Ballell, L. / Batt, S. / Veerapen, N. / Futterer, K. / Besra, ...Authors: Richter, A. / Rudolph, I. / Mollmann, U. / Voigt, K. / Chung, C.W. / Singh, O.M.P. / Rees, M. / Mendoza-Losana, A. / Bates, R. / Ballell, L. / Batt, S. / Veerapen, N. / Futterer, K. / Besra, G. / Imming, P. / Argyrou, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 339.2 KB | Display | ![]() |
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PDB format | ![]() | 274.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 32.1 KB | Display | |
Data in CIF | ![]() | 43.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6hezC ![]() 6hf0C ![]() 6hfvC ![]() 6hfwC ![]() 4fdpS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 52391.332 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P9WJF1, decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.26 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 24 - 34 % w/v polypropylene glcyol 400, 100 mM imidazole |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 19, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97631 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→84.1 Å / Num. obs: 51086 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.4 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4FDP Resolution: 2.2→76.113 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0.71 / Phase error: 29.75 / 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: 38.028 Å2 / ksol: 0.312 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.2→76.113 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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