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- PDB-7u6o: Glutamine Synthetase Type III from Ostreococcus tauri -

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Basic information

Entry
Database: PDB / ID: 7u6o
TitleGlutamine Synthetase Type III from Ostreococcus tauri
ComponentsGlutamine synthetase
KeywordsLIGASE / hexamer / glutamine
Function / homology
Function and homology information


glutamine synthetase / glutamine synthetase activity / :
Similarity search - Function
Glutamine synthetase type III N-terminal / Glutamine synthetase, C-terminal / Glutamine synthetase type III N terminal / Glutamine synthetase C-terminal domain / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase, catalytic domain / Glutamine synthetase, catalytic domain / Glutamine synthetase, catalytic domain / Glutamine synthetase/guanido kinase, catalytic domain
Similarity search - Domain/homology
glutamine synthetase
Similarity search - Component
Biological speciesOstreococcus tauri (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsNovikova, I.V. / Powell, S.M. / Evans, J.E.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)66382 United States
Department of Energy (DOE, United States)74915 United States
CitationJournal: To Be Published
Title: Eukaryotic Glutamine Synthetase Type III Assembles as a Hexamer and Lacks Ring-Ring Quaternary Contacts.
Authors: Novikova, I.V. / Powell, S.M. / Smallwood, C.R. / Purvine, S.O. / Zhou, M. / Evans, J.E.
History
DepositionMar 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamine synthetase
B: Glutamine synthetase
C: Glutamine synthetase
D: Glutamine synthetase
E: Glutamine synthetase
F: Glutamine synthetase


Theoretical massNumber of molelcules
Total (without water)480,5886
Polymers480,5886
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry, Native mass spectrometry confirmed that it is a stable hexamer.
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Glutamine synthetase


Mass: 80098.070 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ostreococcus tauri (plant) / Gene: BE221DRAFT_61941 / Production host: Triticum aestivum (bread wheat) / References: UniProt: A0A1Y5I5Q4, glutamine synthetase

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: A hexamer complex of eukaryotic glutamine synthetase type III
Type: CELL / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Ostreococcus tauri (plant)
Source (recombinant)Organism: Triticum aestivum (bread wheat)
Buffer solutionpH: 7.5
SpecimenConc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm
Image recordingElectron dose: 100 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 270133 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00331488
ELECTRON MICROSCOPYf_angle_d0.57842636
ELECTRON MICROSCOPYf_dihedral_angle_d4.1874284
ELECTRON MICROSCOPYf_chiral_restr0.0414632
ELECTRON MICROSCOPYf_plane_restr0.0045622

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