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- EMDB-43229: Phosphate-bound Vanadium-dependent Bromoperoxidase from Corallina... -

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Basic information

Entry
Database: EMDB / ID: EMD-43229
TitlePhosphate-bound Vanadium-dependent Bromoperoxidase from Corallina pilulifera
Map data
Sample
  • Complex: Phosphate-bound Vanadium-dependent Bromoperoxidase from Corallina pilulifera
    • Protein or peptide: Vanadium-dependent bromoperoxidase
  • Ligand: CALCIUM ION
  • Ligand: PHOSPHATE ION
  • Ligand: water
KeywordsVHPO / VBPO / Vanadium-dependent bromoperoxidase / vanadate-dependent bromoperoxidase / haloperoxidase / 12-mer / electrophilic brominating enzyme / enzyme / OXIDOREDUCTASE
Function / homologybromide peroxidase / bromide peroxidase activity / Bromoperoxidase/chloroperoxidase C-terminal / : / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily / metal ion binding / Vanadium-dependent bromoperoxidase
Function and homology information
Biological speciesCorallina pilulifera (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.19 Å
AuthorsHessefort LZ / Williams DR / Biegasiewicz KF
Funding support United States, 1 items
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 LZ / Williams DR / Biegasiewicz KF
History
DepositionDec 29, 2023-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43229.png

Downloads & links

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Map

FileDownload / File: emd_43229.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 512 pix.
= 527.36 Å		1.03 Å/pix.
x 512 pix.
= 527.36 Å		1.03 Å/pix.
x 512 pix.
= 527.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.1
Minimum - Maximum-4.315826 - 8.930153000000001
Average (Standard dev.)0.0017710715 (±0.17003188)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 527.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_43229_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_43229_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Phosphate-bound Vanadium-dependent Bromoperoxidase from Corallina...

EntireName: Phosphate-bound Vanadium-dependent Bromoperoxidase from Corallina pilulifera
Components
  • Complex: Phosphate-bound Vanadium-dependent Bromoperoxidase from Corallina pilulifera
    • Protein or peptide: Vanadium-dependent bromoperoxidase
  • Ligand: CALCIUM ION
  • Ligand: PHOSPHATE ION
  • Ligand: water

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Supramolecule #1: Phosphate-bound Vanadium-dependent Bromoperoxidase from Corallina...

SupramoleculeName: Phosphate-bound Vanadium-dependent Bromoperoxidase from Corallina pilulifera
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Corallina pilulifera (eukaryote)
Molecular weightTheoretical: 829.60356 KDa

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Macromolecule #1: Vanadium-dependent bromoperoxidase

MacromoleculeName: Vanadium-dependent bromoperoxidase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: bromide peroxidase
Source (natural)Organism: Corallina pilulifera (eukaryote)
Molecular weightTheoretical: 69.19925 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MASMTGGQQM GRGSEFMGIP ADNLQSRAKA SFDTRVAAAE LALNRGVVPS FANGEELLYR NPDPDNTDP SFIASFTKGL PHDDNGAIID PDDFLAFVRA INSGDEKEIA DLTLGPARDP ETGLPIWRSD LANSLELEVR G WENSSAGL ...String:
MGSSHHHHHH SSGLVPRGSH MASMTGGQQM GRGSEFMGIP ADNLQSRAKA SFDTRVAAAE LALNRGVVPS FANGEELLYR NPDPDNTDP SFIASFTKGL PHDDNGAIID PDDFLAFVRA INSGDEKEIA DLTLGPARDP ETGLPIWRSD LANSLELEVR G WENSSAGL TFDLEGPDAQ SIAMPPAPVL TSPELVAEIA ELYLMALGRE IEFSEFDSPK NAEYIQFAID QLNGLEWFNT PA KLGDPPA EIRRRRGEVT VGNLFRGILP GSEVGPYLSQ YIIVGSKQIG SATVGNKTLV SPNAADEFDG EIAYGSITIS QRV RIATPG RDFMTDLKVF LDVQDAADFR GFESYEPGAR LIRTIRDLAT WVHFDALYEA YLNACLILLA NGVPFDPNLP FQQE DKLDN QDVFVNFGSA HVLSLVTEVA TRALKAVRYQ KFNIHRRLRP EATGGLISVN KIAPQKGESI FPEVDLAVEE LGDIL EKAE ISNRKQNIAD GDPDPDPSFL LPMAFAEGSP FHPSYGSGHA VVAGACVTIL KAFFDSGIEI DQVFEVDKDE DKLVKS SFK GTLTVAGELN KLADNIAIGR NMAGVHYFSD QFESLLLGEQ VAIGILEEQS LTYGENFFFN LPKFDGTTIQ I

UniProtKB: Vanadium-dependent bromoperoxidase

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #3: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 8 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.5 / Component - Concentration: 95.0 mM / Component - Formula: NaCl / Component - Name: NaCl
Details: 25 mM pH 6.5 PIPES/NaOH buffer, 2.5 mM CaCl2, 95 mM NaCl
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Details: Approx. 2 μm holes
VitrificationCryogen name: ETHANE / Chamber temperature: 22 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 8.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: -0.8 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 195069
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: T (tetrahedral) / Resolution.type: BY AUTHOR / Resolution: 2.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.1) / Number images used: 195069
Initial angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 4.3.1)
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 4.3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model / Details: Collabfold
DetailsRounds of automatic real space refine in PHENIX with manual real space refine in coot
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

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

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