|Entry||Database: PDB / ID: 1ucu|
|Title||R-type straight flagellar filament made of full-length flagellin|
|Keywords||STRUCTURAL PROTEIN / FLAGELLIN / FLAGELLAR FILAMENT / HELICAL RECONSTRUCTION / Structural protein|
|Specimen source||Salmonella typhimurium / bacteria / サルモネラ・ティフィムリウム, ネズミチフス菌|
|Method||Electron microscopy (4 Å resolution / Filament / Helical)|
|Authors||Yonekura, K. / Maki-Yonekura, S. / Namba, K.|
|Citation||Nature, 2003, 424, 643-650|
#1. NATURE, 2001, 410, 331-337
SummaryFull reportAbout validation report
|Date||Deposition: Apr 22, 2003 / Release: Aug 12, 2003|
|Remark 244||OTHER_DETAILS: REPEAT DISTANCE (ANGSTROMS) : 1698.8 BASIC HELIX INDEX (N10, L10) : ( 11, 4) (N01, L01) : ( -5, 31) SELECTION RULE : L = 66 N + 361 M MAXIMUM BESSEL ORDER : 170 NUMBER OF LAYER-LINES : 298 NUMBER OF FILAMENT IMAGES : 102 NUMBER OF MOLECULAR IMAGES : 41,469 EFFECTIVE RESOLUTION (ANGSTROMS) : 4.000 ALONG THE MERIDIAN EFFECTIVE RESOLUTION (ANGSTROMS) : 5.000 ALONG THE EQUATOR|
|Remark 650||HELIX Determination method: Author determined|
|Remark 700||SHEET Determination method: Author determined|
Downloads & links
A: phase 1 Flagellin
Mass: 51551.203 Da / Num. of mol.: 1 / Mutation: A449V
Source: (natural) Salmonella typhimurium / bacteria / サルモネラ・ティフィムリウム, ネズミチフス菌
References: UniProt: P06179
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: FILAMENT / Reconstruction method: HELICAL|
|Component||Name: R-TYPE STRAIGHT FLAGELLAR FILAMENT / Type: COMPLEX|
|Buffer solution||Name: 150MM NACL, 2MM MGCL2, 20MM TRIS-HCL, 2-5% GLYCEROL|
Details: 150MM NACL, 2MM MGCL2, 20MM TRIS-HCL, 2-5% GLYCEROL
|Specimen||Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Details: QUANTIFOIL R1.2/1.3 (25 NM THICK)|
*PLUSTemp unit: unknown / Method: unknown
-Electron microscopy imaging
|Microscopy||Microscope model: JEOL 3000SFF|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELD / Nominal magnification: 50000 / Calibrated magnification: 47600 / Nominal defocus max: 2200 nm / Nominal defocus min: 1100 nm / Cs: 1.6 mm|
|Specimen holder||Temperature: 4 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.|
|Image recording||Electron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM|
|EM software||Name: X-PLOR / Category: MODEL FITTING|
|CTF correction||Details: BOTH AMPLITUDE AND PHASE|
|3D reconstruction||Method: HELICAL RECONSTRUCTION / Resolution: 4 Å / Number of particles: 102 / Nominal pixel size: 1 / Actual pixel size: 1.05|
Magnification calibration: R-TYPE STRAIGHT FLAGELLAR FILAMENT
Details: The atomic model of a flagellin fragment F41 from Samatey et al (2001) NATURE 410 331-337 (PDB ENTRY 1IO1) was fitted to the density map using O. Then, initial model of full-length flagellin was built by tracing missing terminal chains. The model was refined using both positional and simulated annealing refinements, by a molecular dynamics refinement program, FEX-PLOR, which we developed based on FX-PLOR for EM image analysis of the helical assembly. The amplitude-weighted phase-residual was implemented as an effective potential energy. The layer-line amplitude distributions of the EM data were then scaled to the structure factors calculated from the model based on their radial amplitude profiles obtained by averaging the amplitudes within each resolution shell. The density map was calculated again, and model building and refinement were iterated.
Symmetry type: HELICAL
|Atomic model building||Details: REFINEMENT PROTOCOL--POSITIONAL AND SIMULATED ANNEALING|
Ref protocol: FLEXIBLE FIT / Ref space: RECIPROCAL / Target criteria: amplitude-weighted phase residual
|Atomic model building||PDB-ID: 1IO1|
|Least-squares process||R factor R work: 0.3 / Highest resolution: 4 Å / Lowest resolution: 30 Å|
|Refine hist #LAST||Highest resolution: 4 Å / Lowest resolution: 30 Å|
|Number of atoms included #LAST||Protein: 3617 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 3617|
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