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Negative stain EM Map of the AAA protein CbbX, a red-type Rubisco activase from R. sphaeroides
by single particle reconstruction, at 21 A resolution
#1: Surface view with section colored by density value, Surface level: 0.017, Made by UCSF CHIMERA
#2: Surface view colored by cylindrical radius, Surface level: 0.017, Made by UCSF CHIMERA
#3: Surface view with fitted model, atomic models: PDB-3zuh, Surface level: 0.017, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1932 |
|---|---|
| Title | Negative stain EM Map of the AAA protein CbbX, a red-type Rubisco activase from R. sphaeroides |
| Map | Negative stain EM reconstruction of the R. sphaeroides CbbX hexamer |
| Sample | R. sphaeroides CbbX 3D density map. |
| Keywords |  AAA+ protein, ATPase, Rubisco activase |
| Authors | Mueller-Cajar O, Stotz M, Wendler P, Hartl FU, Bracher A, Hayer-Hartl M |
| Date | Deposition: 2011-07-18, Header release: 2011-08-26, Map release: 2011-11-03, Last update: 2012-09-26 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 0.017, Made by UCSF CHIMERA #2: Surface view colored by cylindrical radius, Surface level: 0.017, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-3zuh, Surface level: 0.017, Made by UCSF CHIMERA |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article Fit: output model of fitting |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Map | |||||||||||||||||||||||||
| File |  EMD-1932.map ( map file in CCP4 format, 8390 KB ) | ||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
| ||||||||||||||||||||||||
| Data Type | Image stored as Reals | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
| ||||||||||||||||||||||||
| Unit Cell | A= B= C: 423.68 A Alpha=beta=gamma: 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X= Y= Z: 3.31 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | Negative stain EM reconstruction of the R. sphaeroides CbbX hexamer | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | R. sphaeroides CbbX 3D density map. |
|---|---|
| Number of Components | 1 |
| Oligomeric State | Hexamer |
| Theoretical Mass | 0.206MDa |
| Component #1: protein - CbbX | |
| Scientific name | Rubisco Activase |
| Common Name | CbbX |
| Theoretical Mass | 0.206 MDa |
| Details | The protein is bound to Ribulose-1,5-bisphosphate, ATP and ATPgammaS |
| Oligomeric Details | Hexamer |
| Number of Copies | 6 |
| Scientific Name of Species | Rhodobacter sphaeroides |
| NCBI taxonomy | 1063 |
| Recombinant expression | Yes |
| Engineered Source | Vector: pHue NCBI taxonomy: 469008 Expression system: Escherichia coli BL21(DE3) |
| Links | Gene Ontology: GO:0005524 |
 Experiment | |
| Sample Preparation | |
| Staining | Grids with adsorbed protein stained with 2% (w/v) uranyl acetate for 40 seconds. |
|---|---|
| Specimen Conc | 0.072 mg/ml |
| Specimen Support Details | plain carbon grid |
| Specimen State | particle |
| Buffer | Details: 20 mM Tris pH 8.0, 50 mM NaCl, 5mM MgCl2, 1mM Ribulose-1,5-bisphosphate, 1mM ATP/ATPgammaS pH: 8 |
| Vitrification | |
| Cryogen Name | NONE |
| Instrument | NONE |
| Imaging | |
| Microscope | FEI TECNAI 12 |
| Date | 19-Nov-2010 |
| Electron Gun | |
| Electron Source | LAB6 |
| Accelerating Voltage | 120 kV |
| Electron Dose | 20 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 90600, Calibrated: 90600 |
| Astigmatism | objective lens astigmatism was corrected for at 110k magnification |
| Nominal Cs | 2 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 260 nm - 1800 nm |
| Specimen Holder | |
| Holder | Eucentric |
| Model | SIDE ENTRY, EUCENTRIC |
| Camera | |
| Detector | Eagle 2k CCD |
 Processing | |
| Method | single particle reconstruction |
|---|---|
| 3D reconstruction | |
| Algorithm | angular reconstitution |
| Software | MRC, IMAGIC, SPIDER |
| CTF Correction | phase flipping, each particle |
| Resolution By Author | 21 A |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| Number of Projections | 245 |
| Atomic Model Fitting | |
| Model #0 | |
| Details | Protocol: rigid body |
| Refinement Protocol | rigid body |
| Refinement Space | REAL |
| PDB Entry ID | 3SYL |
| Model #1 | |
| Refinement Space | REAL |
| Refinement Protocol | rigid body |
| Details | Protocol: rigid body |
| PDB Entry ID | 3CF3 |
| Fitted Coordinate | |
| PDB entry ID | |
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