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- EMDB-71844: Structure of holo vanadium-dependent haloperoxidase from Enhygrom... -

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Basic information

Entry
Database: EMDB / ID: EMD-71844
TitleStructure of holo vanadium-dependent haloperoxidase from Enhygromyxa salina bound to vanadate, and bromide
Map data
Sample
  • Complex: vanadium-dependent haloperoxidase from Enhygromyxa salina bound to vanadate, and bromide
    • Protein or peptide: Vanadium-dependent haloperoxidase
  • Ligand: VANADATE ION
  • Ligand: water
Keywordsvanadium haloperoxidase / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


peroxidase activity
Similarity search - Function
: / Domain of unknown function (DUF6851) / : / VCPO second helical-bundle domain / Bromoperoxidase/chloroperoxidase C-terminal / : / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Vanadium-dependent haloperoxidase
Similarity search - Component
Biological speciesEnhygromyxa salina (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsLoerch S / Baumgartner JT / Balasco Serrao VH / McKinnie SMK
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM147235 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R24GM154185 United States
CitationJournal: To Be Published
Title: Separation of halide oxidation and substrate halogenation chemistries rationalizes site-selective vanadium dependent haloperoxidase catalysis
Authors: Baumgartner JT / Varga LA / Calhoun JT / Balasco Serrao VH / Loerch S / McKinnie SMK
History
DepositionJul 29, 2025-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71844.png

Downloads & links

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Map

FileDownload / File: emd_71844.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 324 pix.
= 270.54 Å		0.84 Å/pix.
x 324 pix.
= 270.54 Å		0.84 Å/pix.
x 324 pix.
= 270.54 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.835 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.25
Minimum - Maximum-5.5857844 - 22.568014000000002
Average (Standard dev.)-0.003968213 (±0.21944235)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 270.53998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71844_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71844_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_71844_half_map_2.map
Projections & Slices
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Sample components

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Entire : vanadium-dependent haloperoxidase from Enhygromyxa salina bound t...

EntireName: vanadium-dependent haloperoxidase from Enhygromyxa salina bound to vanadate, and bromide
Components
  • Complex: vanadium-dependent haloperoxidase from Enhygromyxa salina bound to vanadate, and bromide
    • Protein or peptide: Vanadium-dependent haloperoxidase
  • Ligand: VANADATE ION
  • Ligand: water

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Supramolecule #1: vanadium-dependent haloperoxidase from Enhygromyxa salina bound t...

SupramoleculeName: vanadium-dependent haloperoxidase from Enhygromyxa salina bound to vanadate, and bromide
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Enhygromyxa salina (bacteria)
Molecular weightTheoretical: 148 KDa

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Macromolecule #1: Vanadium-dependent haloperoxidase

MacromoleculeName: Vanadium-dependent haloperoxidase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Enhygromyxa salina (bacteria)
Molecular weightTheoretical: 59.329547 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MQSTRFSTSS SLLLLGALAT AACDPTLDPA ATRVAASDEG VNDQECTTLL PANVPGLQAQ LPTQTMGAD FDFDTGNAPI EIVIPAVLPV IAGSVAPGDA TIVLRFTTML SNAWFDATAP YHPTAVGVYS NLGRRPASES T THANMNIA ...String:
MGSSHHHHHH SSGLVPRGSH MQSTRFSTSS SLLLLGALAT AACDPTLDPA ATRVAASDEG VNDQECTTLL PANVPGLQAQ LPTQTMGAD FDFDTGNAPI EIVIPAVLPV IAGSVAPGDA TIVLRFTTML SNAWFDATAP YHPTAVGVYS NLGRRPASES T THANMNIA ILYASYRTLN SLAPQHAADW DALMVSLGLD PHDDHESTTD PIGIGNAAAA ALLAVRENDG FNQLGFEGGR EY NPIPYAD YTGYEPRNTR FEIKDERRWQ PAIVTSRYGI TRAQHFVTPQ YALTLPYSYD DPQDFGVPLP DKSLKKGSHA KKK YRAQAD EVLEVSANLT DEQKVTAELF EDKIRSLGFS ALFVSLSSGH SLLDFVHYDF LTNLAAFDVG IVVWQEKTQY DAVR PFTAI RHIYGDDEIT AWGGPGQGTV NDLPANEWRS YLDVADHPEY PSASAAFCAA HAQASRLFLG TDDLGWTVPI PAGSS IVEP AITPAADLNL HFPTFTDFAT RCGYSRLWGG VHFEDAILAS FELGDEIGAG AYEFVQAHID GTPP

UniProtKB: Vanadium-dependent haloperoxidase

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Macromolecule #2: VANADATE ION

MacromoleculeName: VANADATE ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: VO4
Molecular weightTheoretical: 114.939 Da
Chemical component information

ChemComp-VN3:
VANADATE ION

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 24 / 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

Concentration0.6 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
50.0 mMHEPES-KOH
300.0 mMPotassium chlorideKCl
100.0 uMsodium vanadateNa3VO4
20.0 mMPotassium chlorideKBr
GridModel: UltrAuFoil / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: 1.5 sec blotting time.
DetailsData was collected at 0.6 mg/ml and 0.06 mg/ml

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 13651 / Average electron dose: 45.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm
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: 27873297
CTF correctionSoftware - Name: cisTEM / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 1249149
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cisTEM
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cisTEM
Final 3D classificationNumber classes: 3 / Software - Name: cisTEM
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9ptr:
Structure of holo vanadium-dependent haloperoxidase from Enhygromyxa salina bound to vanadate, and bromide

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