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- PDB-6uew: Rubisco / CsoS2 N-peptide complex responsible for alpha-carboxyso... -

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Basic information

Entry
Database: PDB / ID: 6uew
TitleRubisco / CsoS2 N-peptide complex responsible for alpha-carboxysome cargo loading
Components
  • Ribulose bisphosphate carboxylase large chain, CsoS2 N-peptide fusion
  • Ribulose bisphosphate carboxylase small chain
KeywordsPROTEIN BINDING / Rubisco / CsoS2 / carboxysome / phase separation
Function / homology
Function and homology information


carboxysome / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I ...Ribulose bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain / Alpha-Beta Plaits / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribulose bisphosphate carboxylase large chain / Ribulose bisphosphate carboxylase small subunit
Similarity search - Component
Biological speciesHalothiobacillus neapolitanus (bacteria)
Halothiobacillus neapolitanus c2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOltrogge, L.M. / Savage, D.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM129241 United States
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2020
Title: Multivalent interactions between CsoS2 and Rubisco mediate alpha-carboxysome formation.
Authors: Oltrogge, L.M. / Chaijarasphong, T. / Chen, A.W. / Bolin, E.R. / Marqusee, S. / Savage, D.F.
#1: Journal: Biorxiv / Year: 2019
Title: Alpha-carboxysome formation is mediated by the multivalent and disordered protein CsoS2
Authors: Oltrogge, L.M. / Chaijarasphong, T. / Chen, A.W. / Bolin, E.R. / Marqusee, S. / Savage, D.F.
History
DepositionSep 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 18, 2020Group: Database references / Category: citation / citation_author
Revision 1.3Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribulose bisphosphate carboxylase large chain, CsoS2 N-peptide fusion
B: Ribulose bisphosphate carboxylase small chain
C: Ribulose bisphosphate carboxylase large chain, CsoS2 N-peptide fusion
D: Ribulose bisphosphate carboxylase small chain
E: Ribulose bisphosphate carboxylase large chain, CsoS2 N-peptide fusion
F: Ribulose bisphosphate carboxylase small chain
G: Ribulose bisphosphate carboxylase large chain, CsoS2 N-peptide fusion
H: Ribulose bisphosphate carboxylase small chain


Theoretical massNumber of molelcules
Total (without water)276,6288
Polymers276,6288
Non-polymers00
Water12,034668
1
A: Ribulose bisphosphate carboxylase large chain, CsoS2 N-peptide fusion
B: Ribulose bisphosphate carboxylase small chain
C: Ribulose bisphosphate carboxylase large chain, CsoS2 N-peptide fusion
D: Ribulose bisphosphate carboxylase small chain
E: Ribulose bisphosphate carboxylase large chain, CsoS2 N-peptide fusion
F: Ribulose bisphosphate carboxylase small chain
G: Ribulose bisphosphate carboxylase large chain, CsoS2 N-peptide fusion
H: Ribulose bisphosphate carboxylase small chain

A: Ribulose bisphosphate carboxylase large chain, CsoS2 N-peptide fusion
B: Ribulose bisphosphate carboxylase small chain
C: Ribulose bisphosphate carboxylase large chain, CsoS2 N-peptide fusion
D: Ribulose bisphosphate carboxylase small chain
E: Ribulose bisphosphate carboxylase large chain, CsoS2 N-peptide fusion
F: Ribulose bisphosphate carboxylase small chain
G: Ribulose bisphosphate carboxylase large chain, CsoS2 N-peptide fusion
H: Ribulose bisphosphate carboxylase small chain


Theoretical massNumber of molelcules
Total (without water)553,25616
Polymers553,25616
Non-polymers00
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area87100 Å2
ΔGint-304 kcal/mol
Surface area124150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.831, 153.945, 108.063
Angle α, β, γ (deg.)90.000, 124.703, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11C-642-

HOH

21C-709-

HOH

31G-692-

HOH

41G-695-

HOH

51G-702-

HOH

61G-716-

HOH

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Components

#1: Protein
Ribulose bisphosphate carboxylase large chain, CsoS2 N-peptide fusion / RuBisCO large subunit


Mass: 56290.449 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothiobacillus neapolitanus (strain ATCC 23641 / c2) (bacteria), (gene. exp.) Halothiobacillus neapolitanus c2 (bacteria)
Strain: ATCC 23641 / c2 / Gene: cbbL, Hneap_0922 / Production host: Escherichia coli (E. coli)
References: UniProt: O85040, ribulose-bisphosphate carboxylase
#2: Protein
Ribulose bisphosphate carboxylase small chain / RuBisCO small subunit


Mass: 12866.575 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothiobacillus neapolitanus (strain ATCC 23641 / c2) (bacteria)
Strain: ATCC 23641 / c2 / Gene: cbbS, rbcS, Hneap_0921 / Production host: Escherichia coli (E. coli)
References: UniProt: P45686, ribulose-bisphosphate carboxylase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 668 / 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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 400, magnesium chloride, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 5, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 2.4→104.1 Å / Num. obs: 90035 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 32.79 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1244 / Rpim(I) all: 0.05064 / Rrim(I) all: 0.1345 / Net I/σ(I): 12.84
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.5876 / Mean I/σ(I) obs: 2.97 / Num. unique obs: 8960 / CC1/2: 0.92 / Rpim(I) all: 0.2497 / Rrim(I) all: 0.6396 / % possible all: 99.92

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling
Coot0.8.9model building
PHENIX1.13_2998phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SVD

1svd


Resolution: 2.4→104.08 Å / SU ML: 0.312 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.2779
RfactorNum. reflection% reflection
Rfree0.2589 1429 1.59 %
Rwork0.1878 --
obs0.189 89949 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 41.8 Å2
Refinement stepCycle: LAST / Resolution: 2.4→104.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17636 0 0 668 18304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007818090
X-RAY DIFFRACTIONf_angle_d0.880924518
X-RAY DIFFRACTIONf_chiral_restr0.05012566
X-RAY DIFFRACTIONf_plane_restr0.00583205
X-RAY DIFFRACTIONf_dihedral_angle_d7.05510606
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.490.31471440.23568810X-RAY DIFFRACTION99.88
2.49-2.590.38941450.23618788X-RAY DIFFRACTION99.81
2.59-2.70.33411400.22578835X-RAY DIFFRACTION99.89
2.7-2.850.28831390.21488843X-RAY DIFFRACTION99.96
2.85-3.020.29681370.21268852X-RAY DIFFRACTION99.92
3.02-3.260.24741490.20798814X-RAY DIFFRACTION99.94
3.26-3.590.25251430.18568884X-RAY DIFFRACTION99.98
3.59-4.10.26691480.16778858X-RAY DIFFRACTION99.97
4.1-5.170.2081400.15248864X-RAY DIFFRACTION99.86
5.17-104.080.21971440.17668972X-RAY DIFFRACTION99.7

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