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Yorodumi- PDB-4lnk: B. subtilis glutamine synthetase structures reveal large active s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lnk | ||||||
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Title | B. subtilis glutamine synthetase structures reveal large active site conformational changes and basis for isoenzyme specific regulation: structure of GS-glutamate-AMPPCP complex | ||||||
Components | Glutamine synthetase | ||||||
Keywords | LIGASE / alpha-beta | ||||||
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 / glutamine biosynthetic process / glutamine synthetase activity / glutamate binding / DNA-binding transcription factor binding / negative regulation of DNA-templated transcription ...cellular response to nitrogen levels / glutamine binding / nitrogen catabolite repression of transcription / negative regulation of core promoter binding / glutamine synthetase / 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: 2.87 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lnk.cif.gz | 529.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lnk.ent.gz | 435 KB | Display | PDB format |
PDBx/mmJSON format | 4lnk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ln/4lnk ftp://data.pdbj.org/pub/pdb/validation_reports/ln/4lnk | HTTPS FTP |
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-Related structure data
Related structure data | 4lnfC 4lniC 4lnnSC 4lnoC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#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 |
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-Non-polymers , 5 types, 84 molecules
#2: Chemical | ChemComp-GLU / #3: Chemical | ChemComp-ADP / #4: Chemical | ChemComp-MG / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.3 % |
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Crystal grow | Temperature: 298 K / pH: 6.8 Details: 10% PEG, 15 mM magnesium chloride, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 |
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 twin | Operator: -1/2*h+1/2*k,3/2*h+1/2*k,-l / Fraction: 0.278 |
Reflection | Resolution: 2.87→120.07 Å / Num. all: 72956 / Num. obs: 72956 / % possible obs: 91 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rsym value: 0.11 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.87→3.03 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.528 / % possible all: 69.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4LNN Resolution: 2.87→120.065 Å / Isotropic thermal model: RESTRAINED / σ(F): 0 / Phase error: 34.89 / Stereochemistry target values: TWIN_LSQ_F / Details: BULK SOLVENT MODEL USED
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.248 Å2 / ksol: 0.325 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.87→120.065 Å
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Refine LS restraints |
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LS refinement shell |
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