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- EMDB-28965: Glutamine synthetase from Pseudomonas aeruginosa, filament double... -

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Basic information

Entry
Database: EMDB / ID: EMD-28965
TitleGlutamine synthetase from Pseudomonas aeruginosa, filament double-unit in compressed conformation
Map data
Sample
  • Complex: P. aeruginosa GS filament.
    • Protein or peptide: Glutamine synthetase
Keywordsglutamine biosynthetic process nitrogen utilization / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / LIGASE
Function / homology
Function and homology information


nitrogen utilization / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / ATP binding / membrane / metal ion binding / cytoplasm
Similarity search - Function
Glutamine synthetase class-I, adenylation site / Glutamine synthetase class-I adenylation site. / Glutamine synthetase type I / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase (GS) catalytic domain profile. / 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 class-I, adenylation site / Glutamine synthetase class-I adenylation site. / Glutamine synthetase type I / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase (GS) catalytic domain profile. / 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, N-terminal domain / Glutamine synthetase, N-terminal domain superfamily / 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 speciesPseudomonas aeruginosa (bacteria) / Pseudomonas aeruginosa PAO1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsPhan IQ / Staker B / Shek R / Moser TH / Evans JE / van Voorhis WC / Myler PJ / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1 items
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 IQ / Staker B / Shek R / Moser TH / Evans JE / van Voorhis WC / Myler PJ
History
DepositionNov 29, 2022-
Header (metadata) releaseFeb 14, 2024-
Map releaseFeb 14, 2024-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28965.png

Downloads & links

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Map

FileDownload / File: emd_28965.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.34927508 - 0.97470754
Average (Standard dev.)0.0040861787 (±0.05132798)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_28965_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_28965_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : P. aeruginosa GS filament.

EntireName: P. aeruginosa GS filament.
Components
  • Complex: P. aeruginosa GS filament.
    • Protein or peptide: Glutamine synthetase

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Supramolecule #1: P. aeruginosa GS filament.

SupramoleculeName: P. aeruginosa GS filament. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Filament formation during sample preparation.
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1

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Macromolecule #1: Glutamine synthetase

MacromoleculeName: Glutamine synthetase / type: protein_or_peptide / ID: 1 / Number of copies: 28 / Enantiomer: LEVO / EC number: glutamine synthetase
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 53.039711 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MAHHHHHHMS YKSHQLIKDH DVKWVDLRFT DTKGKQQHVT MPARDALDDE FFEAGKMFDG SSIAGWKGIE ASDMILMPDD STAVLDPFT EEPTLILVCD IIEPSTMQGY ERDPRNIAKR AEEYLKSTGI GDTVFVGPEP EFFIFDEVKF KSDISGSMFK I FSEQASWN ...String:
MAHHHHHHMS YKSHQLIKDH DVKWVDLRFT DTKGKQQHVT MPARDALDDE FFEAGKMFDG SSIAGWKGIE ASDMILMPDD STAVLDPFT EEPTLILVCD IIEPSTMQGY ERDPRNIAKR AEEYLKSTGI GDTVFVGPEP EFFIFDEVKF KSDISGSMFK I FSEQASWN TDADIESGNK GHRPGVKGGY FPVPPVDHDH EIRTAMCNAL EEMGLVVEVH HHEVATAGQN EIGVKFNTLV AK ADEVQTL KYCVHNVADA YGKTVTFMPK PLYGDNGSGM HVHMSISKDG KNTFAGEGYA GLSETALYFI GGIIKHGKAL NGF TNPSTN SYKRLVPGFE APVMLAYSAR NRSASIRIPY VSSPKARRIE ARFPDPAANP YLAFAALLMA GLDGIQNKIH PGDA ADKNL YDLPPEEAKE IPQVCGSLKE ALEELDKGRA FLTKGGVFTD EFIDAYIELK SEEEIKVRTF VHPLEYDLYY SV

UniProtKB: Glutamine synthetase

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7
Component:
ConcentrationNameFormula
20.0 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
300.0 mMsodium chlorideNaClSodium chloride
1.0 mMtris(2-carboxyethyl)phosphine
5.0 %glycerol

Details: Buffer components of purified protein, final vitrification diluted 50/50 with water.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.3 µm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
In silico model: Single chain modeled with TrRoseTTA was fit into map and the 28-mer model was built in Phenix using NCS operators. The model was refined iteratively using ISOLDE and Phenix Refine + Coot.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: ISOLDE (ver. 1.4)
Details: CryoSPARC GSFSC: no mask 3.3A, loose 3.0A, tight 2.8A, corrected 2.8A.
Number images used: 346920

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 62 / Target criteria: Cross-correlation coefficient
Output model

PDB-8fbp:
Glutamine synthetase from Pseudomonas aeruginosa, filament double-unit in compressed conformation

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