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- PDB-8omc: Y345F/F347Y/Y389F Variant of Dye Type Peroxidase Aa (DtpAa) from ... -

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Basic information

Entry
Database: PDB / ID: 8omc
TitleY345F/F347Y/Y389F Variant of Dye Type Peroxidase Aa (DtpAa) from Streptomyces lividans
ComponentsDeferrochelatase
KeywordsOXIDOREDUCTASE / Heme peroxidase / dye-decolourising peroxidase
Function / homology
Function and homology information


iron import into cell / cell envelope / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / lyase activity / heme binding / metal ion binding / cytosol
Similarity search - Function
Deferrochelatase / : / : / Dyp-type peroxidase, C-terminal / Dyp-type peroxidase, N-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Deferrochelatase
Similarity search - Component
Biological speciesStreptomyces lividans 1326 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLucic, M. / Worrall, J.A.R. / Hough, M.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chem Sci / Year: 2023
Title: New insights into controlling radical migration pathways in heme enzymes gained from the study of a dye-decolorising peroxidase.
Authors: Lucic, M. / Wilson, M.T. / Pullin, J. / Hough, M.A. / Svistunenko, D.A. / Worrall, J.A.R.
History
DepositionMar 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deferrochelatase
B: Deferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7004
Polymers88,4672
Non-polymers1,2332
Water11,674648
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-64 kcal/mol
Surface area25820 Å2
Unit cell
Length a, b, c (Å)71.852, 67.930, 74.483
Angle α, β, γ (deg.)90.00, 105.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Deferrochelatase


Mass: 44233.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans 1326 (bacteria) / Gene: SLI_2602 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7U9DT46
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 648 / 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: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1:1 RATIO OF A 15 MG/ML PROTEIN SOLUTION WITH A PRECIPITANT SOLUTION CONTAINING 20% PEG 6000, 100 MM HEPES PH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→58.26 Å / Num. obs: 110533 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.049 / Rrim(I) all: 0.092 / Net I/σ(I): 10.9
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.336 / Num. unique obs: 5452 / CC1/2: 0.558 / Rpim(I) all: 0.84 / Rrim(I) all: 1.582

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
Aimlessdata scaling
xia2data reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→58.26 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.598 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18922 5468 4.9 %RANDOM
Rwork0.16078 ---
obs0.1622 105042 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.962 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20.12 Å2
2---1.2 Å2-0 Å2
3---0.74 Å2
Refinement stepCycle: 1 / Resolution: 1.5→58.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5579 0 0 648 6227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0125872
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165177
X-RAY DIFFRACTIONr_angle_refined_deg2.0051.6698019
X-RAY DIFFRACTIONr_angle_other_deg0.6851.57112001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9915748
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.431058
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11510824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.10.2839
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.027066
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021286
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2392.0082977
X-RAY DIFFRACTIONr_mcbond_other2.2372.0072976
X-RAY DIFFRACTIONr_mcangle_it2.9143.0083730
X-RAY DIFFRACTIONr_mcangle_other2.9153.0083731
X-RAY DIFFRACTIONr_scbond_it3.1932.2082895
X-RAY DIFFRACTIONr_scbond_other3.1942.2082893
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3963.2184289
X-RAY DIFFRACTIONr_long_range_B_refined5.40826.466546
X-RAY DIFFRACTIONr_long_range_B_other5.36425.7216443
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 406 -
Rwork0.288 7693 -
obs--99.99 %

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