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- PDB-8ool: Glutamine synthetase from Methanothermococcus thermolithotrophicu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ool | |||||||||
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Title | Glutamine synthetase from Methanothermococcus thermolithotrophicus with TbXo4 at a resolution of 1.65 A | |||||||||
![]() | Glutamine synthetase from Methanothermococcus thermolithotrophicus | |||||||||
![]() | LIGASE / Nitrogen-assimilation / methanogenic archaea / allosteric activation / hydrogenotrophic / thermophile / marine / crystallophore / glutamate / ATP | |||||||||
Function / homology | TERBIUM(III) ION![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Mueller, M.-C. / Wagner, T. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Differences in regulation mechanisms of glutamine synthetases from methanogenic archaea unveiled by structural investigations. Authors: Muller, M.C. / Lemaire, O.N. / Kurth, J.M. / Welte, C.U. / Wagner, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 17.4 MB | Display | ![]() |
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Full document | ![]() | 17.3 MB | Display | |
Data in XML | ![]() | 121.3 KB | Display | |
Data in CIF | ![]() | 182.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8oonC ![]() 8oooC ![]() 8ooqC ![]() 8oowC ![]() 8ooxC ![]() 8oozC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 50296.039 Da / Num. of mol.: 6 / Source method: isolated from a natural source Source: (natural) ![]() Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: DSM 2095 / Tissue: / / References: glutamine synthetase #2: Chemical | ChemComp-TB / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / | #5: 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: 2.55 Å3/Da / Density % sol: 51.8 % / Description: Hexagonal plate |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Crystallization was performed in an anoxic tent (with a gas phase of 95% N2/5% H2) on a 96-well two-drop MRC crystallization plate in polystyrene (Molecular Dimensions, Suffolk, UK). The ...Details: Crystallization was performed in an anoxic tent (with a gas phase of 95% N2/5% H2) on a 96-well two-drop MRC crystallization plate in polystyrene (Molecular Dimensions, Suffolk, UK). The sitting drops contained a mix of 0.7 ml of the glutamine synthetase at 15 mg/ml with 10 mM TbXo4 and 0.7 ml of precipitant solution (35 % Pentaerythritol ethoxylate (15/4 EO/OH), 200 mM Ammonium sulphate, 100 mM HEPES pH 7.5). PH range: / |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→49.78 Å / Num. obs: 361584 / % possible obs: 98.9 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.039 / Rrim(I) all: 0.074 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.918 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 51999 / CC1/2: 0.782 / Rpim(I) all: 0.566 / Rrim(I) all: 1.081 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Refinement was performed with PHENIX in combination with fast automatic visual model building in COOT. Refinement was performed with considering all atoms except water anisotropic. ...Details: Refinement was performed with PHENIX in combination with fast automatic visual model building in COOT. Refinement was performed with considering all atoms except water anisotropic. Additionally, riding hydrogens were added during the refinement.
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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 mean: 33.52 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→49.78 Å
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Refine LS restraints |
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LS refinement shell |
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