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- PDB-8vix: Hydrogen Peroxide-bound Vanadium-dependent Bromoperoxidase from C... -

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Basic information

Entry
Database: PDB / ID: 8vix
TitleHydrogen Peroxide-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 / hydrogen peroxide
Function / homologybromide peroxidase / bromide peroxidase activity / Bromoperoxidase/chloroperoxidase C-terminal / : / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily / metal ion binding / PEROXIDE ION / VANADATE ION / Vanadium-dependent bromoperoxidase
Function and homology information
Biological speciesCorallina pilulifera (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.31 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
DepositionJan 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2025Provider: 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)138,83710
Polymers138,3992
Non-polymers4388
Water1448
1
A: Vanadium-dependent bromoperoxidase
B: Vanadium-dependent bromoperoxidase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)1,666,038120
Polymers1,660,78224
Non-polymers5,25696
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation11

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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) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O81959, bromide peroxidase
#2: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PER / PEROXIDE ION


Mass: 31.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: 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: Hydrogen Peroxide-bound Vanadium-dependent Bromoperoxidase from Corallina pilulifera
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.829603 MDa / Experimental value: NO
Source (natural)Organism: Corallina pilulifera (eukaryote)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
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 micrometer 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: FEI TITAN 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
SymmetryPoint symmetry: T (tetrahedral)
3D reconstructionResolution: 2.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 349552 / 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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