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- PDB-7not: Crystal structure of Mycobacterium tuberculosis ArgC in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7not | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis ArgC in complex with nicotinamide adenine dinucleotide phosphate (NADP+) and 5-Methoxy-3-indoleacetic acid | ||||||
![]() | N-acetyl-gamma-glutamyl-phosphate reductase | ||||||
![]() | OXIDOREDUCTASE / ArgC / N-acetyl-gamma-glutamyl-phosphate reductase / NAGPR / Arginine biosynthesis | ||||||
Function / homology | ![]() N-acetyl-gamma-glutamyl-phosphate reductase / N-acetyl-gamma-glutamyl-phosphate reductase activity / arginine biosynthetic process / NADP+ binding / NAD binding / protein dimerization activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gupta, P. / Mendes, V. / 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 | ![]() | 488.2 KB | Display | ![]() |
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PDB format | ![]() | 401.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 94.2 KB | Display | |
Data in CIF | ![]() | 128.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nlfC ![]() 7nlnC ![]() 7nloC ![]() 7nlpC ![]() 7nlqC ![]() 7nlrC ![]() 7nlsC ![]() 7nltC ![]() 7nluC ![]() 7nlwC ![]() 7nlxC ![]() 7nlyC ![]() 7nlzC ![]() 7nm0C ![]() 7nn1C ![]() 7nn4C ![]() 7nn7C ![]() 7nn8C ![]() 7nnbC ![]() 7nncC ![]() 7nnfC ![]() 7nniC ![]() 7nnqC ![]() 7nnrC ![]() 7nnvC ![]() 7nnwC ![]() 7nnyC ![]() 7nnzC ![]() 7norC ![]() 7nosC ![]() 7nouC ![]() 7novC ![]() 7np0C ![]() 7nphC ![]() 7npjC ![]() 2i3aS ![]() 2nqtS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35398.121 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: argC, Rv1652, MTCY06H11.17 / Production host: ![]() ![]() References: UniProt: P9WPZ9, N-acetyl-gamma-glutamyl-phosphate reductase #2: Chemical | ChemComp-MYI / ( #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.56 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M Bis-Tris pH 7 17% PEG Smear High 70 mM phosphate/citrate pH 5.6 20% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 30, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.54→63.91 Å / Num. obs: 87548 / % possible obs: 99.3 % / Redundancy: 5.3 % / CC1/2: 0.986 / Rmerge(I) obs: 0.235 / Rpim(I) all: 0.11 / Rrim(I) all: 0.26 / Net I/σ(I): 7.3 / Num. measured all: 463192 / Scaling rejects: 2218 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2I3A, 2NQT Resolution: 2.54→58.436 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.25 / 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: 108.01 Å2 / Biso mean: 54.9656 Å2 / Biso min: 29.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.54→58.436 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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