[English] 日本語
Yorodumi- PDB-4lno: B. subtilis glutamine synthetase structures reveal large active s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lno | ||||||
---|---|---|---|---|---|---|---|
Title | B. subtilis glutamine synthetase structures reveal large active site conformational changes and basis for isoenzyme specific regulation: form two of GS-1 | ||||||
Components | Glutamine synthetase | ||||||
Keywords | LIGASE / alpha/beta / tnra / glnr | ||||||
Function / homology | Function and homology information cellular response to nitrogen levels / glutamine binding / nitrogen catabolite repression of transcription / negative regulation of core promoter binding / glutamine synthetase / polyamine catabolic process / glutamine biosynthetic process / glutamine synthetase activity / glutamate binding / DNA-binding transcription factor binding ...cellular response to nitrogen levels / glutamine binding / nitrogen catabolite repression of transcription / negative regulation of core promoter binding / glutamine synthetase / polyamine catabolic process / glutamine biosynthetic process / glutamine synthetase activity / glutamate binding / DNA-binding transcription factor binding / negative regulation of DNA-templated transcription / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Schumacher, M.A. / Chinnam, N. / Tonthat, N. / Fisher, S. / Wray, L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Structures of the Bacillus subtilis Glutamine Synthetase Dodecamer Reveal Large Intersubunit Catalytic Conformational Changes Linked to a Unique Feedback Inhibition Mechanism. Authors: Murray, D.S. / Chinnam, N. / Tonthat, N.K. / Whitfill, T. / Wray, L.V. / Fisher, S.H. / Schumacher, M.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4lno.cif.gz | 534.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4lno.ent.gz | 439.9 KB | Display | PDB format |
PDBx/mmJSON format | 4lno.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lno_validation.pdf.gz | 509.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4lno_full_validation.pdf.gz | 596.3 KB | Display | |
Data in XML | 4lno_validation.xml.gz | 107.2 KB | Display | |
Data in CIF | 4lno_validation.cif.gz | 146.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ln/4lno ftp://data.pdbj.org/pub/pdb/validation_reports/ln/4lno | HTTPS FTP |
-Related structure data
Related structure data | 4lnfC 4lniC 4lnkC 4lnnC 2bvcS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 50206.906 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: glnA, BSU17460 / Production host: Escherichia coli (E. coli) / References: UniProt: P12425, glutamine synthetase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-GLN / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.04 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG8000, magnesium chloride, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 23, 2012 |
Radiation | Monochromator: KHOZU Double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→71.68 Å / Num. all: 75100 / Num. obs: 75070 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 24.8 Å2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BVC Resolution: 2.9→71.68 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 4071994.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 28.51 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.8 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→71.68 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|