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- PDB-3hyb: Crystal structure of RbcX from Anabaena, crystal form II -

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Basic information

Entry
Database: PDB / ID: 3hyb
TitleCrystal structure of RbcX from Anabaena, crystal form II
ComponentsRbcX protein
KeywordsCHAPERONE / RuBisCO / protein complex assembly
Function / homology
Function and homology information


ribulose bisphosphate carboxylase complex assembly / carboxysome / carbon fixation / protein folding chaperone / photosynthesis / protein homodimerization activity / cytoplasm
Similarity search - Function
RuBisCO chaperone RbcX / Chaperonin-like RbcX / Chaperonin-like RbcX superfamily / RbcX protein / Chaperonin-like RbcX / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RuBisCO chaperone RbcX
Similarity search - Component
Biological speciesAnabaena sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsBracher, A. / Liu, C.
CitationJournal: Nature / Year: 2010
Title: Coupled chaperone action in folding and assembly of hexadecameric Rubisco.
Authors: Cuimin Liu / Anna L Young / Amanda Starling-Windhof / Andreas Bracher / Sandra Saschenbrecker / Bharathi Vasudeva Rao / Karnam Vasudeva Rao / Otto Berninghausen / Thorsten Mielke / F Ulrich ...Authors: Cuimin Liu / Anna L Young / Amanda Starling-Windhof / Andreas Bracher / Sandra Saschenbrecker / Bharathi Vasudeva Rao / Karnam Vasudeva Rao / Otto Berninghausen / Thorsten Mielke / F Ulrich Hartl / Roland Beckmann / Manajit Hayer-Hartl /
Abstract: Form I Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase), a complex of eight large (RbcL) and eight small (RbcS) subunits, catalyses the fixation of atmospheric CO(2) in photosynthesis. The ...Form I Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase), a complex of eight large (RbcL) and eight small (RbcS) subunits, catalyses the fixation of atmospheric CO(2) in photosynthesis. The limited catalytic efficiency of Rubisco has sparked extensive efforts to re-engineer the enzyme with the goal of enhancing agricultural productivity. To facilitate such efforts we analysed the formation of cyanobacterial form I Rubisco by in vitro reconstitution and cryo-electron microscopy. We show that RbcL subunit folding by the GroEL/GroES chaperonin is tightly coupled with assembly mediated by the chaperone RbcX(2). RbcL monomers remain partially unstable and retain high affinity for GroEL until captured by RbcX(2). As revealed by the structure of a RbcL(8)-(RbcX(2))(8) assembly intermediate, RbcX(2) acts as a molecular staple in stabilizing the RbcL subunits as dimers and facilitates RbcL(8) core assembly. Finally, addition of RbcS results in RbcX(2) release and holoenzyme formation. Specific assembly chaperones may be required more generally in the formation of complex oligomeric structures when folding is closely coupled to assembly.
History
DepositionJun 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Sep 6, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: RbcX protein
B: RbcX protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4863
Polymers35,3902
Non-polymers961
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-50 kcal/mol
Surface area12640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.990, 74.990, 123.841
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein RbcX protein


Mass: 17694.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena sp. (bacteria) / Gene: rbcX / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q44212
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.84 Å3/Da / Density % sol: 56.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1 M (NH4)2SO4, 0.1 M Bis-Tris-HCl pH 5.5, 1 % PEG-3350, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→57.51 Å / Num. obs: 18396 / % possible obs: 99.5 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 8.468
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.424.10.3012.51047925820.30197.7
2.42-2.574.70.2033.71159124670.20398.7
2.57-2.755.40.1564.81281923700.156100
2.75-2.975.40.1156.31192322090.115100
2.97-3.255.40.0828.71108020570.082100
3.25-3.645.40.0611.1988618330.06100
3.64-4.25.30.04713.1892716730.047100
4.2-5.145.30.04811.6747814170.048100
5.14-7.275.20.04711.3581211250.047100
7.27-64.964.70.02819.530876630.02899.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å57.51 Å
Translation3 Å57.51 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2peo

2peo


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.897 / WRfactor Rfree: 0.294 / WRfactor Rwork: 0.272 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.81 / SU B: 15.617 / SU ML: 0.188 / SU R Cruickshank DPI: 0.269 / SU Rfree: 0.222 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.253 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.275 937 5.1 %RANDOM
Rwork0.246 ---
obs0.247 18324 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.49 Å2 / Biso mean: 36.305 Å2 / Biso min: 21.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20.15 Å20 Å2
2--0.3 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1768 0 5 44 1817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221880
X-RAY DIFFRACTIONr_angle_refined_deg1.3641.982563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.275244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.17925.06379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.15815330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.467159
X-RAY DIFFRACTIONr_chiral_restr0.0940.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021413
X-RAY DIFFRACTIONr_nbd_refined0.210.2898
X-RAY DIFFRACTIONr_nbtor_refined0.2940.21305
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.255
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2780.210
X-RAY DIFFRACTIONr_mcbond_it0.5011.51235
X-RAY DIFFRACTIONr_mcangle_it0.87321918
X-RAY DIFFRACTIONr_scbond_it1.5183726
X-RAY DIFFRACTIONr_scangle_it2.2814.5645
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 60 -
Rwork0.313 1230 -
all-1290 -
obs--97.51 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.2309-4.1362.62753.4062-2.00851.3282-0.2120.336-0.250.24960.08320.06480.34380.22960.12870.15030.2455-0.0854-0.041-0.0342-0.129631.9698.49611.05
219.2072-3.348310.95022.387-4.593810.24041.17271.1514-1.4344-0.4327-0.9362-0.28011.41341.7105-0.23640.17320.3624-0.05740.59150.0694-0.054528.24114.4722.819
35.5252-3.05842.37557.7298-2.62683.85870.0660.3208-0.49280.33050.14550.19580.3371-0.0587-0.2114-0.09180.1335-0.0519-0.0616-0.0819-0.039529.6357.59516.771
412.3749-12.3815-2.296314.07251.95722.34320.82870.9062-0.631-1.2053-0.49010.78590.05730.1219-0.33860.34460.1442-0.25950.055-0.16-0.07331.5720.33413.759
510.8855-1.0487-2.676312.53865.876710.28450.3751.837-0.3948-2.42-1.40242.5899-0.4794-1.74641.02730.74710.4801-0.51730.6586-0.30410.527334.36-14.6725.133
65.0121-6.02121.727812.4279-2.82053.5816-0.02790.61730.5586-0.1454-0.0199-0.31470.08450.19320.0478-0.01710.1674-0.09410.0467-0.03-0.070439.576.02617.264
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-9 - 41
2X-RAY DIFFRACTION2A42 - 56
3X-RAY DIFFRACTION3A57 - 105
4X-RAY DIFFRACTION4B-9 - 36
5X-RAY DIFFRACTION5B37 - 64
6X-RAY DIFFRACTION6B65 - 105

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