[English] 日本語
![](img/lk-miru.gif)
- EMDB-28965: Glutamine synthetase from Pseudomonas aeruginosa, filament double... -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Glutamine synthetase from Pseudomonas aeruginosa, filament double-unit in compressed conformation | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
![]() | glutamine biosynthetic process nitrogen utilization / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / LIGASE | |||||||||
Function / homology | ![]() nitrogen utilization / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / ATP binding / membrane / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
![]() | Phan IQ / Staker B / Shek R / Moser TH / Evans JE / van Voorhis WC / Myler PJ / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 32.5 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 16.2 KB 16.2 KB | Display Display | ![]() |
Images | ![]() | 82.2 KB | ||
Filedesc metadata | ![]() | 6.1 KB | ||
Others | ![]() ![]() | 59.5 MB 59.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8fbpMC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_28965_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_28965_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : P. aeruginosa GS filament.
Entire | Name: P. aeruginosa GS filament. |
---|---|
Components |
|
-Supramolecule #1: P. aeruginosa GS filament.
Supramolecule | Name: P. aeruginosa GS filament. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Filament formation during sample preparation. |
---|---|
Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Glutamine synthetase
Macromolecule | Name: Glutamine synthetase / type: protein_or_peptide / ID: 1 / Number of copies: 28 / Enantiomer: LEVO / EC number: glutamine synthetase |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 53.039711 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | filament |
-
Sample preparation
Buffer | pH: 7 Component:
Details: Buffer components of purified protein, final vitrification diluted 50/50 with water. | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.3 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
Startup model | Type 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. |
---|---|
Final reconstruction | Applied 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 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2) |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 62 / Target criteria: Cross-correlation coefficient |
---|---|
Output model | ![]() PDB-8fbp: |