[English] 日本語
Yorodumi- PDB-8fbp: Glutamine synthetase from Pseudomonas aeruginosa, filament double... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fbp | ||||||
---|---|---|---|---|---|---|---|
Title | Glutamine synthetase from Pseudomonas aeruginosa, filament double-unit in compressed conformation | ||||||
Components | Glutamine synthetase | ||||||
Keywords | LIGASE / 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 / membrane / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
Authors | Phan, 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
| ||||||
Citation | Journal: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8fbp.cif.gz | 2.1 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8fbp.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8fbp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fbp_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8fbp_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8fbp_validation.xml.gz | 254.5 KB | Display | |
Data in CIF | 8fbp_validation.cif.gz | 394.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/8fbp ftp://data.pdbj.org/pub/pdb/validation_reports/fb/8fbp | HTTPS FTP |
-Related structure data
Related structure data | 28965MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
Other databases |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | 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 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 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 solution | pH: 7 Details: Buffer components of purified protein, final vitrification diluted 50/50 with water. | |||||||||||||||||||||||||
Buffer component |
| |||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 300 nm / C2 aperture diameter: 50 µm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||||||||||||||
CTF correction | Details: Patch-based motion correction / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C7 (7 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 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 building | B value: 62 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|