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- PDB-7dhq: Structure of Halothiobacillus neapolitanus Microcompartments Prot... -

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Basic information

Entry
Database: PDB / ID: 7dhq
TitleStructure of Halothiobacillus neapolitanus Microcompartments Protein CsoS1D
ComponentsMicrocompartments proteinBacterial microcompartment
KeywordsSTRUCTURAL PROTEIN / Microcompartments Protein / CsoS1D
Function / homologyBacterial microcompartment (BMC) circularly permuted domain / Bacterial microcompartment (BMC) circularly permuted domain profile. / carboxysome / Bacterial microcompartment domain / CcmK-like superfamily / BMC / carbon fixation / Carboxysome shell protein CsoS1D
Function and homology information
Biological speciesHalothiobacillus neapolitanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsXue, B. / Tan, Y.Q. / Ali, S. / Robinson, R.C. / Narita, A. / Yew, W.S.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore) Singapore
CitationJournal: Biomacromolecules / Year: 2021
Title: Structure of a Minimal α-Carboxysome-Derived Shell and Its Utility in Enzyme Stabilization.
Authors: Yong Quan Tan / Samson Ali / Bo Xue / Wei Zhe Teo / Lay Hiang Ling / Maybelle Kho Go / Hong Lv / Robert C Robinson / Akihiro Narita / Wen Shan Yew /
Abstract: Bacterial microcompartments are proteinaceous shells that encase specialized metabolic processes in bacteria. Recent advances in simplification of these intricate shells have encouraged ...Bacterial microcompartments are proteinaceous shells that encase specialized metabolic processes in bacteria. Recent advances in simplification of these intricate shells have encouraged bioengineering efforts. Here, we construct minimal shells derived from the α-carboxysome, which we term Cso-shell. Using cryogenic electron microscopy, the atomic-level structures of two shell forms were obtained, reinforcing notions of evolutionarily conserved features in bacterial microcompartment shell architecture. Encapsulation peptide sequences that facilitate loading of heterologous protein cargo within the shells were identified. We further provide a first demonstration in utilizing minimal bacterial microcompartment-derived shells for hosting heterologous enzymes. Cso-shells were found to stabilize enzymatic activities against heat shock, presence of methanol co-solvent, consecutive freeze-thawing, and alkaline environments. This study yields insights into α-carboxysome assembly and advances the utility of synthetic bacterial microcompartments as nanoreactors capable of stabilizing enzymes with varied properties and reaction chemistries.
History
DepositionNov 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: 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 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Microcompartments protein
B: Microcompartments protein
C: Microcompartments protein
D: Microcompartments protein
E: Microcompartments protein
F: Microcompartments protein


Theoretical massNumber of molelcules
Total (without water)150,6816
Polymers150,6816
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17720 Å2
ΔGint-79 kcal/mol
Surface area40010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.074, 70.876, 74.975
Angle α, β, γ (deg.)65.900, 63.400, 77.680
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Microcompartments protein / Bacterial microcompartment


Mass: 25113.578 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothiobacillus neapolitanus (strain ATCC 23641 / c2) (bacteria)
Strain: ATCC 23641 / c2 / Gene: Hneap_0903 / Plasmid: pES2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D0KZ73
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 1.96 Å3/Da / Density % sol: 37.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 1M Ammonium Sulfate, 0.1M Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.49→45.152 Å / Num. obs: 30912 / % possible obs: 92.5 % / Redundancy: 1.776 % / Biso Wilson estimate: 48.402 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.14 / Rrim(I) all: 0.198 / Χ2: 1.074 / Net I/σ(I): 4.64 / Num. measured all: 132842
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.49-2.641.7351.0190.751943613048112050.3181.44185.9
2.64-2.821.7330.7121.12006212242115770.5081.00794.6
2.82-3.041.6270.4231.71755011408107860.7080.59894.5
3.04-3.331.8250.2523.07182421045699950.8690.35795.6
3.33-3.721.8770.1465.4316340955087070.9510.20791.2
3.72-4.291.8740.0917.9714849837279240.9820.12994.6
4.29-5.251.7950.06910.1111914714066390.9870.09893
5.25-7.371.7350.0788.548909549651360.9840.1193.4
7.37-45.1521.9720.03319.645540315028100.9970.04689.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.49 Å45.15 Å
Translation2.49 Å45.15 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.8.3phasing
PHENIX1.18_3845refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FCH

3fch


Resolution: 2.7→45.15 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2711 1470 4.81 %
Rwork0.201 29113 -
obs0.2042 30583 97.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.11 Å2 / Biso mean: 41.6144 Å2 / Biso min: 24.25 Å2
Refinement stepCycle: final / Resolution: 2.7→45.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9456 0 0 145 9601
Biso mean---36.06 -
Num. residues----1227
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.80.3411580.29622866302497
2.8-2.910.34681800.26552889306997
2.91-3.040.35121580.25112888304697
3.04-3.20.30251590.23552925308499
3.2-3.40.32511420.21372967310999
3.4-3.660.27471340.20152884301897
3.66-4.030.25371250.18842914303996
4.03-4.620.2331540.16432944309899
4.62-5.810.22061380.1772957309598
5.81-45.150.22031220.17732879300196

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