+Open data
-Basic information
Entry | Database: PDB / ID: 3syl | ||||||
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Title | Crystal structure of the AAA+ protein CbbX, native structure | ||||||
Components | Protein CbbX | ||||||
Keywords | CHAPERONE / photosynthesis / Rubisco activase / AAA+ protein / calvin cycle | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhodobacter sphaeroides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Mueller-Cajar, O. / Stotz, M. / Wendler, P. / Hartl, F.U. / Bracher, A. / Hayer-Hartl, M. | ||||||
Citation | Journal: Nature / Year: 2011 Title: Structure and function of the AAA+ protein CbbX, a red-type Rubisco activase. Authors: Oliver Mueller-Cajar / Mathias Stotz / Petra Wendler / F Ulrich Hartl / Andreas Bracher / Manajit Hayer-Hartl / Abstract: Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyses the fixation of atmospheric CO(2) in photosynthesis, but tends to form inactive complexes with its substrate ribulose 1,5- ...Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyses the fixation of atmospheric CO(2) in photosynthesis, but tends to form inactive complexes with its substrate ribulose 1,5-bisphosphate (RuBP). In plants, Rubisco is reactivated by the AAA(+) (ATPases associated with various cellular activities) protein Rubisco activase (Rca), but no such protein is known for the Rubisco of red algae. Here we identify the protein CbbX as an activase of red-type Rubisco. The 3.0-Å crystal structure of unassembled CbbX from Rhodobacter sphaeroides revealed an AAA(+) protein architecture. Electron microscopy and biochemical analysis showed that ATP and RuBP must bind to convert CbbX into functionally active, hexameric rings. The CbbX ATPase is strongly stimulated by RuBP and Rubisco. Mutational analysis suggests that CbbX functions by transiently pulling the carboxy-terminal peptide of the Rubisco large subunit into the hexamer pore, resulting in the release of the inhibitory RuBP. Understanding Rubisco activation may facilitate efforts to improve CO(2) uptake and biomass production by photosynthetic organisms. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3syl.cif.gz | 118.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3syl.ent.gz | 91.1 KB | Display | PDB format |
PDBx/mmJSON format | 3syl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3syl_validation.pdf.gz | 454.7 KB | Display | wwPDB validaton report |
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Full document | 3syl_full_validation.pdf.gz | 461.5 KB | Display | |
Data in XML | 3syl_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 3syl_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sy/3syl ftp://data.pdbj.org/pub/pdb/validation_reports/sy/3syl | HTTPS FTP |
-Related structure data
Related structure data | 1932C 3sykSC 3zuhC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | THE ANALYSIS OF THE CBBX PROTEIN IN SOLUTION AND EM STUDIES SUGGEST THAT THE BIOLOGICALLY ACTIVE OLIGOMER IS A HEXAMER, BUT IT CANNOT BE GENERATED BY THE APPLICATION OF SYMMETRY OPERATORS TO THE CHAINS IN THE COORDINATE FILE. |
-Components
#1: Protein | Mass: 34717.289 Da / Num. of mol.: 2 / Mutation: M282I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: KD131 / KCTC 12085 / Gene: cbbX, RSKD131_2679 / Plasmid: pHUE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P95648 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.59 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 6.5 Details: 0.4 M (NH4)2SO4, 0.05 M MES-NaOH pH 6.5, vapor diffusion, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.894→46.098 Å / Num. all: 15101 / Num. obs: 15101 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 15 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3syk Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.843 / WRfactor Rfree: 0.251 / WRfactor Rwork: 0.1954 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7832 / SU B: 20.439 / SU ML: 0.378 / SU Rfree: 0.4879 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.488 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.88 Å2 / Biso mean: 49.6742 Å2 / Biso min: 15.25 Å2
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Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.076 Å / Total num. of bins used: 20
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