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- PDB-7x9w: Sulfur Oxygenase Reductase from Acidianus ambivalens -

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Basic information

Entry
Database: PDB / ID: 7x9w
TitleSulfur Oxygenase Reductase from Acidianus ambivalens
ComponentsSulfur oxygenase/reductase
KeywordsOXIDOREDUCTASE / Thermostable Oxidoreductase
Function / homologysulfur oxygenase/reductase / sulfur oxygenase/reductase activity / Sulphur oxygenase reductase / Sulphur oxygenase reductase / Dimeric alpha-beta barrel / metal ion binding / cytoplasm / : / Sulfur oxygenase/reductase
Function and homology information
Biological speciesAcidianus ambivalens (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsSobhy, M.A. / Hamdan, S.M.
Funding support Saudi Arabia, 1items
OrganizationGrant numberCountry
Other privateURF/1/3764-01-01 Saudi Arabia
CitationJournal: PLoS One / Year: 2022
Title: Cryo-electron structures of the extreme thermostable enzymes Sulfur Oxygenase Reductase and Lumazine Synthase.
Authors: Mohamed A Sobhy / Lingyun Zhao / Dalaver Anjum / Ali Behzad / Masateru Takahashi / Muhammad Tehseen / Alfredo De Biasio / Rachid Sougrat / Samir Hamdan /
Abstract: Thermostable enzymes have the potential for use in a wide variety of biotechnological applications. Cryo-electron microscopy (cryo-EM) enables the imaging of biomolecules in their native aqueous ...Thermostable enzymes have the potential for use in a wide variety of biotechnological applications. Cryo-electron microscopy (cryo-EM) enables the imaging of biomolecules in their native aqueous environment. Here, we present high resolution cryo-EM structures of two thermostable enzymes that exhibit multimeric cage-like structures arranged into two different point-group symmetries. First, we determined the structure of the Sulfur Oxygenase Reductase (SOR) enzyme that catalyzes both the oxygenation and disproportionation of elemental sulfur in Archea and is composed of 24 homomeric units each of MW ≃ 35 kDa arranged in octahedral symmetry. The structure of SOR from Acidianus ambivalens (7X9W) was determined at 2.78 Å resolution. The active site of each subunit inside the central nanocompartment is composed of Fe3+ coordinated to two water molecules and the three amino acids (H86, H90 and E114). Second, we determined the structure of Lumazine Synthase (LS) from Aquifex aeolicus (7X7M) at 2.33 Å resolution. LS forms a cage-like structure consisting of 60 identical subunits each of MW ≃ 15 kDa arranged in a strict icosahedral symmetry. The LS subunits are interconnected by ion-pair network. Due to their thermostability and relatively easy purification scheme, both SOR and LS can serve as a model for the catalytic and structural characterization of biocatalysts as well as a benchmark for cryo-EM sample preparation, optimization of the acquisition parameters and 3D reconstruction.
History
DepositionMar 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulfur oxygenase/reductase
B: Sulfur oxygenase/reductase
C: Sulfur oxygenase/reductase
D: Sulfur oxygenase/reductase
E: Sulfur oxygenase/reductase
F: Sulfur oxygenase/reductase
G: Sulfur oxygenase/reductase
H: Sulfur oxygenase/reductase
I: Sulfur oxygenase/reductase
J: Sulfur oxygenase/reductase
K: Sulfur oxygenase/reductase
L: Sulfur oxygenase/reductase
M: Sulfur oxygenase/reductase
N: Sulfur oxygenase/reductase
O: Sulfur oxygenase/reductase
P: Sulfur oxygenase/reductase
Q: Sulfur oxygenase/reductase
R: Sulfur oxygenase/reductase
S: Sulfur oxygenase/reductase
T: Sulfur oxygenase/reductase
U: Sulfur oxygenase/reductase
V: Sulfur oxygenase/reductase
W: Sulfur oxygenase/reductase
X: Sulfur oxygenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)844,42648
Polymers843,08524
Non-polymers1,34024
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Sulfur oxygenase/reductase / Sulfur oxygenase reductase / SOR


Mass: 35128.555 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidianus ambivalens (archaea) / Gene: sor / Production host: Escherichia coli (E. coli) / References: UniProt: P29082, sulfur oxygenase/reductase
#2: Chemical...
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: CryoEM structure of Sulfur Oxygenase Reductase composed of 24 identical subunits
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Acidianus ambivalens (archaea)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris hydrochlorideTris.HCl1
2150 mMsodium chlorideNaCl1
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K
Details: The purified protein was applied to the glow discharged grids inside the chamber, blotted for a duration of 1.5 s, and then plunge-frozen in liquid ethane cooled by liquid nitrogen.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 68 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 20

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM softwareName: RELION / Category: 3D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 391093
Details: particles were selected by LoG picking from 800 micrographs
SymmetryPoint symmetry: O (octahedral)
3D reconstructionResolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 207550 / Num. of class averages: 1 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00761344
ELECTRON MICROSCOPYf_angle_d0.74283208
ELECTRON MICROSCOPYf_dihedral_angle_d17.48722776
ELECTRON MICROSCOPYf_chiral_restr0.0518736
ELECTRON MICROSCOPYf_plane_restr0.00710680

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