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- PDB-8fbp: Glutamine synthetase from Pseudomonas aeruginosa, filament double... -

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Basic information

Entry
Database: PDB / ID: 8fbp
TitleGlutamine synthetase from Pseudomonas aeruginosa, filament double-unit in compressed conformation
ComponentsGlutamine synthetase
KeywordsLIGASE / glutamine biosynthetic process nitrogen utilization / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


nitrogen utilization / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / ATP binding / metal ion binding / membrane / cytoplasm
Similarity search - Function
Glutamine synthetase class-I, adenylation site / Glutamine synthetase class-I adenylation site. / Glutamine synthetase type I / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase, N-terminal domain superfamily ...Glutamine synthetase class-I, adenylation site / Glutamine synthetase class-I adenylation site. / Glutamine synthetase type I / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / 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
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsPhan, I.Q. / Staker, B. / Shek, R. / Moser, T.H. / Evans, J.E. / van Voorhis, W.C. / Myler, P.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: Glutamine synthetase from Pseudomonas aeruginosa, filament double-unit in compressed conformation
Authors: Phan, I.Q. / Staker, B. / Shek, R. / Moser, T.H. / Evans, J.E. / van Voorhis, W.C. / Myler, P.J.
History
DepositionNov 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release

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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
G: Glutamine synthetase
H: Glutamine synthetase
I: Glutamine synthetase
J: Glutamine synthetase
K: Glutamine synthetase
L: Glutamine synthetase
M: Glutamine synthetase
N: Glutamine synthetase
O: Glutamine synthetase
P: Glutamine synthetase
Q: Glutamine synthetase
R: Glutamine synthetase
S: Glutamine synthetase
T: Glutamine synthetase
U: Glutamine synthetase
V: Glutamine synthetase
W: Glutamine synthetase
X: Glutamine synthetase
Y: Glutamine synthetase
Z: Glutamine synthetase
a: Glutamine synthetase
b: Glutamine synthetase


Theoretical massNumber of molelcules
Total (without water)1,485,11228
Polymers1,485,11228
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, Oligomerization was inferred from top and side views showing clear chains of 2 x 7 units.
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Glutamine synthetase / GS / Glutamate--ammonia ligase / Glutamine synthetase I beta / GSI beta


Mass: 53039.711 Da / Num. of mol.: 28
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: glnA, PA5119
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9HU65, glutamine synthetase

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: P. aeruginosa GS filament. / Type: COMPLEX / Details: Filament formation during sample preparation. / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7
Details: Buffer components of purified protein, final vitrification diluted 50/50 with water.
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid1
2300 mMsodium chlorideNaCl1
31 mMtris(2-carboxyethyl)phosphine1
45 %glycerol1
SpecimenEmbedding 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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 300 nm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
EM software
IDNameVersionCategoryDetails
1cryoSPARC3.3.2particle selection
4cryoSPARC3.3.2CTF correctionPatch CTF
7ISOLDE1.4model fitting
9cryoSPARC3.3.2initial Euler assignment
10cryoSPARC3.3.2final Euler assignment
12ISOLDE1.43D reconstruction
13PHENIX1.2model refinement
CTF correctionDetails: Patch-based motion correction / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C7 (7 fold cyclic)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 346920
Details: CryoSPARC GSFSC: no mask 3.3A, loose 3.0A, tight 2.8A, corrected 2.8A.
Symmetry type: POINT
Atomic model buildingB value: 62 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00396873
ELECTRON MICROSCOPYf_angle_d0.444130918
ELECTRON MICROSCOPYf_dihedral_angle_d4.72712963
ELECTRON MICROSCOPYf_chiral_restr0.04114194
ELECTRON MICROSCOPYf_plane_restr0.00417107

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