[English] 日本語
Yorodumi- PDB-2wgs: Crystal structure of Mycobacterium Tuberculosis Glutamine Synthet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wgs | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Mycobacterium Tuberculosis Glutamine Synthetase in complex with a purine analogue inhibitor. | ||||||
Components | GLUTAMINE SYNTHETASE 1 | ||||||
Keywords | LIGASE / RELAXED STATE / PURINE ANALOGUE / NUCLEOTIDE-BINDING / GLNA1 / MT2278 / RV2220 / CYTOPLASM / SYNTHETASE | ||||||
Function / homology | Function and homology information nitrogen utilization / positive regulation of plasminogen activation / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / zymogen binding / cell wall / fibronectin binding / peptidoglycan-based cell wall / protein homooligomerization ...nitrogen utilization / positive regulation of plasminogen activation / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / zymogen binding / cell wall / fibronectin binding / peptidoglycan-based cell wall / protein homooligomerization / magnesium ion binding / extracellular region / ATP binding / membrane / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Nilsson, M.T. / Krajewski, W.W. / Jones, T.A. / Mowbray, S.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Structural Basis for the Inhibition of Mycobacterium Tuberculosis Glutamine Synthetase by Novel ATP-Competitive Inhibitors. Authors: Nilsson, M.T. / Krajewski, W.W. / Yellagunda, S. / Prabhumurthy, S. / Chamarahally, G.N. / Siddamadappa, C. / Srinivasa, B.R. / Yahiaoui, S. / Larhed, M. / Karlen, A. / Jones, T.A. / Mowbray, S.L. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2005 Title: Structure of Mycobacterium Tuberculosis Glutamine Synthetase in Complex with a Transition-State Mimic Provides Functional Insights. Authors: Krajewski, W.W. / Jones, T.A. / Mowbray, S.L. | ||||||
History |
| ||||||
Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2wgs.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2wgs.ent.gz | 904.1 KB | Display | PDB format |
PDBx/mmJSON format | 2wgs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wgs_validation.pdf.gz | 3.6 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2wgs_full_validation.pdf.gz | 3.7 MB | Display | |
Data in XML | 2wgs_validation.xml.gz | 206.6 KB | Display | |
Data in CIF | 2wgs_validation.cif.gz | 275.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/2wgs ftp://data.pdbj.org/pub/pdb/validation_reports/wg/2wgs | HTTPS FTP |
-Related structure data
Related structure data | 2whiC 1htoS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
|
-Components
#1: Protein | Mass: 54584.730 Da / Num. of mol.: 12 / Fragment: RESIDUES 2-478 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV Description: E. COLI STRAIN GJ4745 IS ADENYLYLTRANSFERASE DEFICIENT (GLNE-) Plasmid: PTRC99C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): GJ4745 References: UniProt: P0A590, UniProt: P9WN39*PLUS, glutamine synthetase #2: Chemical | ChemComp-1AZ / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Sequence details | PROTEIN EXPRESSED IN FUSION WITH A N-TERMINAL 9 AMINO ACID PEPTIDE CONTAINING A SIX HISTIDINE ...PROTEIN EXPRESSED IN FUSION WITH A N-TERMINAL 9 AMINO ACID PEPTIDE CONTAINING | |
---|
-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 % / Description: NONE |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5 Details: EQUAL VOLUMES OF MOTHER LIQUOR (0.1 M SODIUM ACETATE, PH 5, 0.75 M 1,6-HEXANEDIOL) AND PROTEIN SOLUTION (10 G/L IN 0.020 M TRIS-HCL. PH 7.5, 0.15 M SODIUM CHLORIDE, 0.005 M MAGNESIUM ...Details: EQUAL VOLUMES OF MOTHER LIQUOR (0.1 M SODIUM ACETATE, PH 5, 0.75 M 1,6-HEXANEDIOL) AND PROTEIN SOLUTION (10 G/L IN 0.020 M TRIS-HCL. PH 7.5, 0.15 M SODIUM CHLORIDE, 0.005 M MAGNESIUM CHLORIDE, 2%(V/V) DMSO, 0.0002 M INHIBITOR), VAPOR DIFFUSION, HANGING-DROP, TEMPERATURE 294K. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 12, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→29.9 Å / Num. obs: 200628 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.55→2.65 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.8 / % possible all: 95.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HTO Resolution: 2.55→29.95 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.915 / SU B: 10.94 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 1.195 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AMINO ACIDS 63 TO 66 AND 405 TO 412 WERE OMITTED FROM THE STRUCTURE.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.987 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→29.95 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|