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- PDB-9g4t: Beta carbonic anhydrase CsoSCA from the Halothiobacillus neapolit... -

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Basic information

Entry
Database: PDB / ID: 9g4t
TitleBeta carbonic anhydrase CsoSCA from the Halothiobacillus neapolitanus alpha-carboxysome
ComponentsImmunoglobulin G-binding protein G,Carboxysome shell carbonic anhydrase
KeywordsLYASE / Carbonic anhydrase / Carboxysome / rubisco
Function / homology
Function and homology information


carboxysome / carbon fixation / IgG binding / carbonic anhydrase / carbonate dehydratase activity / extracellular region / metal ion binding
Similarity search - Function
Carboxysome shell carbonic anhydrase / Carboxysome shell carbonic anhydrase, N-terminal / Carboxysome shell carbonic anhydrase, C-terminal / : / : / : / Carboxysome Shell Carbonic Anhydrase, C-terminal / Carboxysome Shell Carbonic Anhydrase, catalytic domain / Carboxysome Shell Carbonic Anhydrase, N-terminal / IgG-binding B ...Carboxysome shell carbonic anhydrase / Carboxysome shell carbonic anhydrase, N-terminal / Carboxysome shell carbonic anhydrase, C-terminal / : / : / : / Carboxysome Shell Carbonic Anhydrase, C-terminal / Carboxysome Shell Carbonic Anhydrase, catalytic domain / Carboxysome Shell Carbonic Anhydrase, N-terminal / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain
Similarity search - Domain/homology
Carboxysome shell carbonic anhydrase / Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus sp. 'group G' (bacteria)
Halothiobacillus neapolitanus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.51 Å
AuthorsNg, P.C. / Marles-Wright, J. / Basle, A. / Liu, L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)2599456 United Kingdom
CitationJournal: To Be Published
Title: Beta carbonic anhydrase CsoSCA from the Halothiobacillus neapolitanus alpha-carboxysome
Authors: Ng, P.C. / Marles-Wright, J. / Basle, A. / Liu, L.
History
DepositionJul 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Jul 30, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein G,Carboxysome shell carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3602
Polymers68,2941
Non-polymers651
Water00
1
A: Immunoglobulin G-binding protein G,Carboxysome shell carbonic anhydrase
hetero molecules

A: Immunoglobulin G-binding protein G,Carboxysome shell carbonic anhydrase
hetero molecules

A: Immunoglobulin G-binding protein G,Carboxysome shell carbonic anhydrase
hetero molecules

A: Immunoglobulin G-binding protein G,Carboxysome shell carbonic anhydrase
hetero molecules

A: Immunoglobulin G-binding protein G,Carboxysome shell carbonic anhydrase
hetero molecules

A: Immunoglobulin G-binding protein G,Carboxysome shell carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)410,15812
Polymers409,7666
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5

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Components

#1: Antibody Immunoglobulin G-binding protein G,Carboxysome shell carbonic anhydrase / IgG-binding protein G / CsoSCA / Carbonic anhydrase / CA / Carboxysome shell protein CsoS3


Mass: 68294.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. 'group G' (bacteria), (gene. exp.) Halothiobacillus neapolitanus (bacteria)
Gene: spg, csoS3, ORF1, Hneap_0919 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P06654, UniProt: O85042, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Carbonic anhydrase complex / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.409 MDa / Experimental value: NO
Source (natural)Organism: Halothiobacillus neapolitanus (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMTris/Hydrochloric acidTris/HCl1
2150 mMSodium chlorideNaCl1
31 mMEthylenediaminetetraacetic acidEDTA1
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 240000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5particle selection
2EPUimage acquisition
4cryoSPARC4.5CTF correction
7UCSF ChimeraX1.8model fitting
9cryoSPARC4.5initial Euler assignment
10cryoSPARC4.5final Euler assignment
11cryoSPARC4.5classification
12cryoSPARC4.53D reconstruction
13PHENIX1.21.1model refinement
CTF correctionDetails: Patch CTF in cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1390946
Details: Blob picker with 150 A diameter. Picks verified using inspect picks job.
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 2.51 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 435319 / Algorithm: FOURIER SPACE / Details: Homogeneous refinement in cryoSPARC / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: Model fitting using ChimeraX
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 108.76 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00373663
ELECTRON MICROSCOPYf_angle_d0.56214974
ELECTRON MICROSCOPYf_chiral_restr0.04552
ELECTRON MICROSCOPYf_plane_restr0.0036659
ELECTRON MICROSCOPYf_dihedral_angle_d3.6538507

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