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- PDB-11zs: Cryo EM structure of glutamine synthetase from Brucella melitensis -

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Basic information

Entry
Database: PDB / ID: 11zs
TitleCryo EM structure of glutamine synthetase from Brucella melitensis
ComponentsGlutamine synthetase, catalytic domain
KeywordsLIGASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / glutamine synthetase / Brucella melitensis
Function / homology
Function and homology information


biogenic amine catabolic process / biogenic amine metabolic process / glutamine synthetase / : / glutamine synthetase activity / ATP binding
Similarity search - Function
Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain / Glutamine synthetase, N-terminal domain / Glutamine synthetase, catalytic domain / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, catalytic domain / Glutamine synthetase/guanido kinase, catalytic domain
Similarity search - Domain/homology
Glutamine synthetase, catalytic domain
Similarity search - Component
Biological speciesBrucella abortus 2308 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsLovell, S. / Liu, L. / Hammons, A.M. / Ingham, D.J. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
CitationJournal: To be published
Title: Cryo EM structure of glutamine synthetase from Brucella melitensis
Authors: Lovell, S. / Liu, L. / Hammons, A.M. / Ingham, D.J.
History
DepositionMar 20, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamine synthetase, catalytic domain
B: Glutamine synthetase, catalytic domain
C: Glutamine synthetase, catalytic domain
D: Glutamine synthetase, catalytic domain
E: Glutamine synthetase, catalytic domain
F: Glutamine synthetase, catalytic domain
G: Glutamine synthetase, catalytic domain
H: Glutamine synthetase, catalytic domain
I: Glutamine synthetase, catalytic domain
J: Glutamine synthetase, catalytic domain
K: Glutamine synthetase, catalytic domain
L: Glutamine synthetase, catalytic domain


Theoretical massNumber of molelcules
Total (without water)632,70712
Polymers632,70712
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Glutamine synthetase, catalytic domain


Mass: 52725.621 Da / Num. of mol.: 12 / Fragment: 3-455
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus 2308 (bacteria) / Gene: BAB2_0507 / Plasmid: BrabA.00111.b.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2YKY7, glutamine synthetase
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Dodecameric complex of glutamine synthetase / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Brucella abortus 2308 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
Details: 25 mM HEPES pH 7.0, 500 mM NaCl, 5% Glycerol, 2 mM DTT, 0.025% Azide
SpecimenConc.: 2.09 mg/ml / Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
EM embeddingMaterial: vitreous ice
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 20 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: 4D-STEM / Nominal magnification: 100000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 500 nm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON I (4k x 4k) / Num. of grids imaged: 1
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC5particle selection
2PHENIX2.0_5936model refinement
5cryoSPARC5CTF correction
10cryoSPARC5initial Euler assignment
11cryoSPARC5classification
12cryoSPARC53D reconstruction
Image processingDetails: The selected images were high-pass filtered and normalized
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71284 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: 3D CRYSTAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
RefinementHighest resolution: 3.28 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00243056
ELECTRON MICROSCOPYf_angle_d0.38358224
ELECTRON MICROSCOPYf_dihedral_angle_d9.02115780
ELECTRON MICROSCOPYf_chiral_restr0.0376048
ELECTRON MICROSCOPYf_plane_restr0.0037524

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