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- PDB-8vgx: Phosphate-bound Vanadium-dependent Bromoperoxidase from Corallina... -

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Basic information

Entry
Database: PDB / ID: 8vgx
TitlePhosphate-bound Vanadium-dependent Bromoperoxidase from Corallina pilulifera
ComponentsVanadium-dependent bromoperoxidase
KeywordsOXIDOREDUCTASE / VHPO / VBPO / Vanadium-dependent bromoperoxidase / vanadate-dependent bromoperoxidase / haloperoxidase / 12-mer / electrophilic brominating enzyme / enzyme
Function / homologybromide peroxidase / bromide peroxidase activity / Bromoperoxidase/chloroperoxidase C-terminal / : / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily / metal ion binding / PHOSPHATE ION / Vanadium-dependent bromoperoxidase
Function and homology information
Biological speciesCorallina pilulifera (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.19 Å
AuthorsHessefort, L.Z. / Williams, D.R. / Biegasiewicz, K.F.
Funding support United States, 1items
OrganizationGrant numberCountry
Other government United States
CitationJournal: To be published
Title: High-Resolution CryoEM unveils insights into the Catalytic Mechanism of a Vanadium-dependent Bromoperoxidase
Authors: Hessefort, L.Z. / Williams, D.R. / Biegasiewicz, K.F.
History
DepositionDec 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vanadium-dependent bromoperoxidase
B: Vanadium-dependent bromoperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,6696
Polymers138,3992
Non-polymers2704
Water1448
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Vanadium-dependent bromoperoxidase / V-BPO / Vanadium haloperoxidase


Mass: 69199.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corallina pilulifera (eukaryote) / Plasmid: pET-28a+ / Details (production host): Produced by TwistBioscience / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O81959, bromide peroxidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: Phosphate-bound Vanadium-dependent Bromoperoxidase from Corallina pilulifera
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.82960356 MDa / Experimental value: NO
Source (natural)Organism: Corallina pilulifera (eukaryote)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pET-28a+
Buffer solutionpH: 6.5
Details: 25 mM pH 6.5 PIPES/NaOH buffer, 2.5 mM CaCl2, 95 mM NaCl
Buffer componentConc.: 95 mM / Name: NaCl / Formula: NaCl
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Approx. 2 μm holes / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Chamber temperature: 22 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 22500 X / Nominal defocus max: 2800 nm / Nominal defocus min: -800 nm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 8 sec. / Electron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.3.1particle selection
2SerialEM4.0.25image acquisition
3cryoSPARC4.3.1masking
4CTFFIND4CTF correction
7UCSF ChimeraX1.6model fitting
8PHENIX1.20.1model refinement
9Coot0.9.8.7model refinement
11cryoSPARC4.3.1initial Euler assignment
12cryoSPARC4.3.1final Euler assignment
13cryoSPARC4.3.1classification
14cryoSPARC4.3.13D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 195069
SymmetryPoint symmetry: T (tetrahedral)
3D reconstructionResolution: 2.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 195069 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: Rounds of automatic real space refine in PHENIX with manual real space refine in coot
Atomic model buildingDetails: Collabfold / Source name: AlphaFold / Type: in silico model

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