[English] 日本語
Yorodumi
- PDB-8q20: Crystal structure of Vanadium-dependent haloperoxidase R425D muta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8q20
TitleCrystal structure of Vanadium-dependent haloperoxidase R425D mutant (A. marina)
ComponentsVanadium-dependent bromoperoxidase, putative
KeywordsOXIDOREDUCTASE / Vanadium / Enzyme Catalysis / Peroxidase / Halogenation / Mutant
Function / homologyBromoperoxidase/chloroperoxidase C-terminal / : / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily / peroxidase activity / PHOSPHATE ION / Vanadium-dependent bromoperoxidase, putative
Function and homology information
Biological speciesAcaryochloris marina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsZeides, P. / Bellmannn-Sickert, K. / Zhang, R. / Seel, C.J. / Most, V. / Schroeder, C.T. / Groll, M. / Gulder, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Unraveling the molecular basis of substrate specificity and halogen activation in vanadium-dependent haloperoxidases.
Authors: Zeides, P. / Bellmann-Sickert, K. / Zhang, R. / Seel, C.J. / Most, V. / Schoeder, C.T. / Groll, M. / Gulder, T.
History
DepositionAug 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Mar 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Vanadium-dependent bromoperoxidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2603
Polymers73,0691
Non-polymers1912
Water00
1
A: Vanadium-dependent bromoperoxidase, putative
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)879,11536
Polymers876,82212
Non-polymers2,29224
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation26_555-x,-y,z1
crystal symmetry operation31_555-z,-x,y1
crystal symmetry operation36_555-y,-z,x1
crystal symmetry operation52_555x,-y,-z1
crystal symmetry operation54_555z,-x,-y1
crystal symmetry operation59_555y,-z,-x1
crystal symmetry operation75_555-x,y,-z1
crystal symmetry operation80_555-z,x,-y1
crystal symmetry operation82_555-y,z,-x1
Buried area96890 Å2
ΔGint-621 kcal/mol
Surface area214600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)308.380, 308.380, 308.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number210
Space group name H-MF4132

-
Components

#1: Protein Vanadium-dependent bromoperoxidase, putative


Mass: 73068.539 Da / Num. of mol.: 1 / Mutation: R452D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acaryochloris marina (bacteria) / Gene: AM1_4975 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B0C4R0
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.18 Å3/Da / Density % sol: 70.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M TRIS, 1.25 M Ammoniumdihydrogenphosphate, 0.5 mM potassium vanadate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→30 Å / Num. obs: 15830 / % possible obs: 96.5 % / Redundancy: 5 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 9.4
Reflection shellResolution: 3.5→3.6 Å / Redundancy: 5 % / Rmerge(I) obs: 0.632 / Num. unique obs: 1244 / % possible all: 96.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→30 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.926 / SU B: 54.558 / SU ML: 0.361 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.502 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2443 790 5 %RANDOM
Rwork0.2243 ---
obs0.2253 15012 96.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 160.04 Å2 / Biso mean: 96.498 Å2 / Biso min: 81.59 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 3.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4876 0 10 0 4886
Biso mean--112.54 --
Num. residues----632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0134994
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174473
X-RAY DIFFRACTIONr_angle_refined_deg1.2141.6436782
X-RAY DIFFRACTIONr_angle_other_deg1.0521.57610413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8755630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.96923.143280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10315794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7851531
X-RAY DIFFRACTIONr_chiral_restr0.0370.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025740
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021021
X-RAY DIFFRACTIONr_rigid_bond_restr0.07239465
LS refinement shellResolution: 3.5→3.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 56 -
Rwork0.339 1057 -
all-1113 -
obs--96.53 %
Refinement TLS params.Method: refined / Origin x: 19.9442 Å / Origin y: 4.7943 Å / Origin z: 44.8523 Å
111213212223313233
T0.0344 Å2-0.0178 Å2-0.008 Å2-0.0139 Å20.0005 Å2--0.0089 Å2
L0.1768 °2-0.1152 °2-0.0235 °2-0.1399 °20.0174 °2--0.0827 °2
S0.02 Å °-0.0144 Å °0.0033 Å °0.0247 Å °-0.0142 Å °0.0011 Å °0.0127 Å °0.0099 Å °-0.0058 Å °

+
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