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- PDB-9iz8: fungal unspecific peroxygenase from Thielavia terrestris -

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Basic information

Entry
Database: PDB / ID: 9iz8
Titlefungal unspecific peroxygenase from Thielavia terrestris
ComponentsHeme haloperoxidase family profile domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / fungal unspecific peroxygenase heme oxy-functionalization of carbon biosynthesis
Function / homologyChloroperoxidase / Chloroperoxidase-like superfamily / Peroxidase, family 2 / Heme haloperoxidase family profile. / peroxidase activity / metal ion binding / PROTOPORPHYRIN IX CONTAINING FE / Heme haloperoxidase family profile domain-containing protein
Function and homology information
Biological speciesThermothielavioides terrestris (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsLai, M.Y. / Yu, H.L.
Funding support China, 1items
OrganizationGrant numberCountry
Other government2019YFA0905000 China
CitationJournal: Nat Commun / Year: 2025
Title: Designing an oxidase toolbox for site-directed oxidation of taxanes.
Authors: Lai, M. / Weng, Y. / Wei, J. / Lu, X.Y. / Huang, Z. / Li, H. / Huang, L. / Zhang, Z. / Zhu, L. / Xu, J.H. / Hong, R. / Yu, H.L.
History
DepositionJul 31, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2025Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 4, 2026Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heme haloperoxidase family profile domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0313
Polymers24,3901
Non-polymers6412
Water4,125229
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.474, 67.474, 133.838
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Heme haloperoxidase family profile domain-containing protein / fungal unspecific peroxygenase


Mass: 24390.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermothielavioides terrestris (strain ATCC 38088 / NRRL 8126) (fungus)
Gene: THITE_125074 / Production host: Komagataella pastoris (fungus) / References: UniProt: G2R8M6
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 3.12 Å3/Da / Density % sol: 60.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.6% v/v Dipeptides Mix (2%w/v Ala-Ala, 2%w/v Gly-L-Asp, 2%w/v Ala-Gln, 2%w/v Gly-Sar, 2%w/v Gly-Glu, 2%w/v L-Carnosine, 2%w/v Gly-L-Ala, 2%w/v Leu-Ala hydrate), 0.1 M Morpheus -Buffer ...Details: 1.6% v/v Dipeptides Mix (2%w/v Ala-Ala, 2%w/v Gly-L-Asp, 2%w/v Ala-Gln, 2%w/v Gly-Sar, 2%w/v Gly-Glu, 2%w/v L-Carnosine, 2%w/v Gly-L-Ala, 2%w/v Leu-Ala hydrate), 0.1 M Morpheus -Buffer System 1 pH 6.5 (1M imidazole; MES monohydrate (acid)), 37.5% Precipitant Mix 4 (25% v/v MPD; 25% PEG1000; 25% w/v PEG 3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.54→60.25 Å / Num. obs: 39568 / % possible obs: 85.1 % / Redundancy: 11.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.013 / Rrim(I) all: 0.054 / Χ2: 0.79 / Net I/σ(I): 24.7 / Num. measured all: 470568
Reflection shellResolution: 1.54→1.63 Å / % possible obs: 27.1 % / Redundancy: 1.2 % / Rmerge(I) obs: 0.406 / Num. measured all: 2185 / Num. unique obs: 1772 / CC1/2: 0.682 / Rpim(I) all: 0.384 / Rrim(I) all: 0.56 / Χ2: 0.58 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
PHENIX(???)refinement
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→29.98 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2006 1947 4.93 %
Rwork0.1895 --
obs0.19 39474 85.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.54→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1726 0 44 229 1999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d15.496640
X-RAY DIFFRACTIONf_chiral_restr0.049266
X-RAY DIFFRACTIONf_plane_restr0.01329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.620.3866590.30271147X-RAY DIFFRACTION37
1.62-1.670.2785910.26181899X-RAY DIFFRACTION61
1.79-1.860.20921530.20233076X-RAY DIFFRACTION99
1.86-1.940.22971660.20653134X-RAY DIFFRACTION100
1.94-2.040.24891730.18973114X-RAY DIFFRACTION100
2.05-2.170.21711440.17563159X-RAY DIFFRACTION100
2.17-2.340.20122010.17843099X-RAY DIFFRACTION100
2.34-2.580.20631520.18373173X-RAY DIFFRACTION100

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