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- PDB-3syl: Crystal structure of the AAA+ protein CbbX, native structure -

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Basic information

Entry
Database: PDB / ID: 3syl
TitleCrystal structure of the AAA+ protein CbbX, native structure
ComponentsProtein CbbX
KeywordsCHAPERONE / photosynthesis / Rubisco activase / AAA+ protein / calvin cycle
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding
Similarity search - Function
CbxX/CfxQ, monofunctional / CbxX/CfxQ / CbbX, AAA lid domain / AAA lid domain / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities ...CbxX/CfxQ, monofunctional / CbxX/CfxQ / CbbX, AAA lid domain / AAA lid domain / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMueller-Cajar, O. / Stotz, M. / Wendler, P. / Hartl, F.U. / Bracher, A. / Hayer-Hartl, M.
CitationJournal: 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
DepositionJul 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2011Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Nov 20, 2019Group: Database references / Category: pdbx_database_related / struct_ref_seq_dif
Item: _pdbx_database_related.content_type / _pdbx_database_related.db_id / _struct_ref_seq_dif.details
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein CbbX
B: Protein CbbX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0118
Polymers69,4352
Non-polymers5766
Water41423
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-110 kcal/mol
Surface area26660 Å2
MethodPISA
2
A: Protein CbbX
hetero molecules

B: Protein CbbX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0118
Polymers69,4352
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_466x-1/2,-y+3/2,-z+11
Buried area3030 Å2
ΔGint-107 kcal/mol
Surface area27620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.128, 93.141, 106.102
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsTHE 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.

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Components

#1: Protein Protein CbbX


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 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.59 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3-3.163.80.4531.7827821920.45397.8
3.16-3.353.80.2862.7790420940.28698.1
3.35-3.593.80.1794.2732119410.17997.7
3.59-3.873.80.1096.9683518070.10997.2
3.87-4.243.80.06811632816710.06896.6
4.24-4.743.80.04915.1568815100.04996.7
4.74-5.483.70.04715.5499313410.04796.3
5.48-6.713.70.05214424611440.05295.9
6.71-9.493.60.02427.832308860.02494.5
9.49-46.0983.50.01542.117995150.01593.6

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.2854 777 5.2 %RANDOM
Rwork0.2184 ---
all0.2218 14794 --
obs0.2218 14233 96.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.88 Å2 / Biso mean: 49.6742 Å2 / Biso min: 15.25 Å2
Baniso -1Baniso -2Baniso -3
1--2 Å20 Å20 Å2
2--2.46 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4296 0 30 23 4349
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0214393
X-RAY DIFFRACTIONr_angle_refined_deg1.0841.9785962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1945571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82623.158190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.815676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0561537
X-RAY DIFFRACTIONr_chiral_restr0.0690.2683
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023333
X-RAY DIFFRACTIONr_nbd_refined0.2060.22112
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22984
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2173
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.24
X-RAY DIFFRACTIONr_mcbond_it0.3891.52900
X-RAY DIFFRACTIONr_mcangle_it0.71624488
X-RAY DIFFRACTIONr_scbond_it0.72531627
X-RAY DIFFRACTIONr_scangle_it1.2514.51474
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 56 -
Rwork0.281 1026 -
all-1082 -
obs--96.78 %

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