[English] 日本語
Yorodumi
- EMDB-43270: Hydrogen Peroxide-bound Vanadium-dependent Bromoperoxidase from C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-43270
TitleHydrogen Peroxide-bound Vanadium-dependent Bromoperoxidase from Corallina pilulifera
Map data
Sample
  • Complex: Hydrogen Peroxide-bound Vanadium-dependent Bromoperoxidase from Corallina pilulifera
    • Protein or peptide: Vanadium-dependent bromoperoxidase
  • Ligand: VANADATE ION
  • Ligand: PEROXIDE ION
  • Ligand: CALCIUM ION
  • Ligand: water
KeywordsVHPO / VBPO / Vanadium-dependent bromoperoxidase / vanadate-dependent bromoperoxidase / haloperoxidase / 12-mer / electrophilic brominating enzyme / enzyme / hydrogen peroxide / 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: 2.31 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
DepositionJan 5, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43270.png

Downloads & links

-
Map

FileDownload / File: emd_43270.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: 0.8
Minimum - Maximum-9.107642 - 16.65014
Average (Standard dev.)-0.00032598883 (±0.23585552)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: #2

Fileemd_43270_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_43270_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Hydrogen Peroxide-bound Vanadium-dependent Bromoperoxidase from C...

EntireName: Hydrogen Peroxide-bound Vanadium-dependent Bromoperoxidase from Corallina pilulifera
Components
  • Complex: Hydrogen Peroxide-bound Vanadium-dependent Bromoperoxidase from Corallina pilulifera
    • Protein or peptide: Vanadium-dependent bromoperoxidase
  • Ligand: VANADATE ION
  • Ligand: PEROXIDE ION
  • Ligand: CALCIUM ION
  • Ligand: water

-
Supramolecule #1: Hydrogen Peroxide-bound Vanadium-dependent Bromoperoxidase from C...

SupramoleculeName: Hydrogen Peroxide-bound Vanadium-dependent Bromoperoxidase from Corallina pilulifera
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Corallina pilulifera (eukaryote)
Molecular weightTheoretical: 829.603 KDa

-
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

-
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

-
Macromolecule #3: PEROXIDE ION

MacromoleculeName: PEROXIDE ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: PER
Molecular weightTheoretical: 31.999 Da
Chemical component information

ChemComp-PER:
PEROXIDE ION

-
Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 8 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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 micrometer holes
VitrificationCryogen name: ETHANE / Chamber temperature: 22 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN 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

+
Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: T (tetrahedral) / Resolution.type: BY AUTHOR / Resolution: 2.31 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.1) / Number images used: 349552
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)

-
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-8vix:
Hydrogen Peroxide-bound Vanadium-dependent Bromoperoxidase from Corallina pilulifera

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more