[English] 日本語
Yorodumi- PDB-7nph: Crystal structure of Mycobacterium tuberculosis ArgC in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nph | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Mycobacterium tuberculosis ArgC in complex with 5-methoxy-1,3-benzoxazole-2-carboxylic acid | ||||||
Components | N-acetyl-gamma-glutamyl-phosphate reductase | ||||||
Keywords | OXIDOREDUCTASE / ArgC / N-acetyl-gamma-glutamyl-phosphate reductase / NAGPR / Arginine biosynthesis | ||||||
Function / homology | Function and homology information N-acetyl-gamma-glutamyl-phosphate reductase / N-acetyl-gamma-glutamyl-phosphate reductase activity / L-arginine biosynthetic process / NADP+ binding / NAD binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å | ||||||
Authors | Gupta, P. / Mendes, V. / Blundell, T.L. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Comput Struct Biotechnol J / Year: 2021 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7nph.cif.gz | 475.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7nph.ent.gz | 386 KB | Display | PDB format |
PDBx/mmJSON format | 7nph.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nph_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7nph_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7nph_validation.xml.gz | 94.1 KB | Display | |
Data in CIF | 7nph_validation.cif.gz | 128.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/7nph ftp://data.pdbj.org/pub/pdb/validation_reports/np/7nph | 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 7notC 7nouC 7novC 7np0C 7npjC 2i3aS 2nqtS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 36485.305 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: argC, Rv1652, MTCY06H11.17 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P9WPZ9, N-acetyl-gamma-glutamyl-phosphate reductase #2: Chemical | ChemComp-UKE / | #3: Chemical | ChemComp-PO4 / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.32 % |
---|---|
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 | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å | ||||||||||||||||||||||||||||||
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: 2.57→69.593 Å / Num. obs: 86043 / % possible obs: 100 % / Redundancy: 5.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.034 / Rrim(I) all: 0.082 / Net I/σ(I): 11 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2I3A, 2NQT Resolution: 2.57→69.59 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 38.87 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 135.01 Å2 / Biso mean: 81.6685 Å2 / Biso min: 20 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.57→69.59 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|