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Yorodumi- PDB-6z1e: Crystal structure of the AAA domain of Rubisco Activase from Nost... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6z1e | ||||||
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Title | Crystal structure of the AAA domain of Rubisco Activase from Nostoc sp. (strain PCC 7120) | ||||||
Components | Ribulose bisphosphate carboxylase/oxygenase activase | ||||||
Keywords | CHAPERONE / AAA+ domain | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Nostoc sp. PCC 7120 = FACHB-418 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.454 Å | ||||||
Authors | Popilka, L. / Bracher, A. | ||||||
Citation | Journal: Cell / Year: 2020 Title: Dual Functions of a Rubisco Activase in Metabolic Repair and Recruitment to Carboxysomes. Authors: Mirkko Flecken / Huping Wang / Leonhard Popilka / F Ulrich Hartl / Andreas Bracher / Manajit Hayer-Hartl / Abstract: Rubisco, the key enzyme of CO fixation in photosynthesis, is prone to inactivation by inhibitory sugar phosphates. Inhibited Rubisco undergoes conformational repair by the hexameric AAA+ chaperone ...Rubisco, the key enzyme of CO fixation in photosynthesis, is prone to inactivation by inhibitory sugar phosphates. Inhibited Rubisco undergoes conformational repair by the hexameric AAA+ chaperone Rubisco activase (Rca) in a process that is not well understood. Here, we performed a structural and mechanistic analysis of cyanobacterial Rca, a close homolog of plant Rca. In the Rca:Rubisco complex, Rca is positioned over the Rubisco catalytic site under repair and pulls the N-terminal tail of the large Rubisco subunit (RbcL) into the hexamer pore. Simultaneous displacement of the C terminus of the adjacent RbcL opens the catalytic site for inhibitor release. An alternative interaction of Rca with Rubisco is mediated by C-terminal domains that resemble the small Rubisco subunit. These domains, together with the N-terminal AAA+ hexamer, ensure that Rca is packaged with Rubisco into carboxysomes. The cyanobacterial Rca is a dual-purpose protein with functions in Rubisco repair and carboxysome organization. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z1e.cif.gz | 313.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z1e.ent.gz | 260.4 KB | Display | PDB format |
PDBx/mmJSON format | 6z1e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6z1e_validation.pdf.gz | 788.2 KB | Display | wwPDB validaton report |
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Full document | 6z1e_full_validation.pdf.gz | 791.6 KB | Display | |
Data in XML | 6z1e_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 6z1e_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z1/6z1e ftp://data.pdbj.org/pub/pdb/validation_reports/z1/6z1e | HTTPS FTP |
-Related structure data
Related structure data | 6hasC 6z1dSC 6z1fC 6z1gC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32773.316 Da / Num. of mol.: 2 / Fragment: AAA+ domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc sp. PCC 7120 = FACHB-418 (bacteria) Gene: rca, alr1533 / Plasmid: pHUE / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): pBAD33-EcGroSEL / References: UniProt: P58555 #2: Chemical | #3: Chemical | ChemComp-ADP / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.65 Å3/Da / Density % sol: 53.59 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7 / Details: 2.2 M Na-acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.13956 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 9, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.13956 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.454→47.388 Å / Num. all: 25855 / Num. obs: 25855 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 67.16 Å2 / Rpim(I) all: 0.016 / Rrim(I) all: 0.042 / Rsym value: 0.038 / Net I/av σ(I): 16.5 / Net I/σ(I): 29.3 / Num. measured all: 171034 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Z1D Resolution: 2.454→28.749 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.59
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 199.33 Å2 / Biso mean: 76.01 Å2 / Biso min: 35.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.454→28.749 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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