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- PDB-7nlw: Crystal structure of Mycobacterium tuberculosis ArgB in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7nlw | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis ArgB in complex with 2-(5-methoxy-1H-indol-3-yl)acetonitrile | ||||||
![]() | Acetylglutamate kinase | ||||||
![]() | TRANSFERASE / ArgB / Acetylglutamate kinase | ||||||
Function / homology | ![]() acetylglutamate kinase / acetylglutamate kinase activity / arginine biosynthetic process via ornithine / arginine biosynthetic process / peptidoglycan-based cell wall / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Mendes, V. / Thomas, S.E. / Cory-Wright, J. / Blundell, T.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A fragment-based approach to assess the ligandability of ArgB, ArgC, ArgD and ArgF in the L-arginine biosynthetic pathway of Mycobacterium tuberculosis Authors: Gupta, P. / Thomas, S.E. / Zaidan, S.A. / Pasillas, M.A. / Cory-Wright, J. / Sebastian-Perez, V. / Burgess, A. / Cattermole, E. / Meghir, C. / Abell, C. / Coyne, A.G. / Jacobs, W.R. / ...Authors: Gupta, P. / Thomas, S.E. / Zaidan, S.A. / Pasillas, M.A. / Cory-Wright, J. / Sebastian-Perez, V. / Burgess, A. / Cattermole, E. / Meghir, C. / Abell, C. / Coyne, A.G. / Jacobs, W.R. / Blundell, T.L. / Tiwari, S. / Mendes, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.7 KB | Display | ![]() |
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PDB format | ![]() | 95.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7nlfC ![]() 7nlnC ![]() 7nloC ![]() 7nlpC ![]() 7nlqC ![]() 7nlrC ![]() 7nlsC ![]() 7nltC ![]() 7nluC ![]() 7nlxC ![]() 7nlyC ![]() 7nlzC ![]() 7nm0C ![]() 7nn1C ![]() 7nn4C ![]() 7nn7C ![]() 7nn8C ![]() 7nnbC ![]() 7nncC ![]() 7nnfC ![]() 7nniC ![]() 7nnqC ![]() 7nnrC ![]() 7nnvC ![]() 7nnwC ![]() 7nnyC ![]() 7nnzC ![]() 7norC ![]() 7nosC ![]() 7notC ![]() 7nouC ![]() 7novC ![]() 7np0C ![]() 7nphC ![]() 7npjC ![]() 2ap9S S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 31212.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: argB, Rv1654, MTCY06H11.19 / Production host: ![]() ![]() | ||||
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#2: Chemical | ChemComp-UOK / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 63.93 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 9.5 Details: 1260 mM ammonium sulphate 100 mM CHES pH 9.5 200 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.32→87.18 Å / Num. obs: 18318 / % possible obs: 99.7 % / Redundancy: 8.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.026 / Rrim(I) all: 0.076 / Net I/σ(I): 14.8 / Num. measured all: 157958 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2AP9 Resolution: 2.32→26.2 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 132.98 Å2 / Biso mean: 89.132 Å2 / Biso min: 58.39 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.32→26.2 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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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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