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- PDB-9tm7: Unspecific Peroxygenase from Daldinia childiae -

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Basic information

Entry
Database: PDB / ID: 9tm7
TitleUnspecific Peroxygenase from Daldinia childiae
ComponentsUnspecific Peroxygenase
KeywordsOXIDOREDUCTASE / Heme / Unspecific Peroxygenase
Function / homologyPROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesDaldinia childiae (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsMcKenzie, A. / Clark, C. / Melling, B. / Domenech, J. / Grogan, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Rsc Chem Biol / Year: 2026
Title: Structure, characterisation and application of an unspecific peroxygenase from Daldinia childiae .
Authors: McKenzie, A. / Clark, C. / Cornish, K.A.S. / Li, J. / Domenech, J. / Melling, B. / Ralston, M.P.H. / Cartwright, J. / Mulholland, N.P. / Unsworth, W.P. / Grogan, G.
History
DepositionDec 12, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2026Group: Database references / Derived calculations / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Unspecific Peroxygenase
B: Unspecific Peroxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4847
Polymers61,1782
Non-polymers1,3065
Water3,405189
1
A: Unspecific Peroxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2303
Polymers30,5891
Non-polymers6412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Unspecific Peroxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2544
Polymers30,5891
Non-polymers6653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.604, 78.049, 62.585
Angle α, β, γ (deg.)90.00, 95.18, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-453-

HOH

21A-505-

HOH

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Components

#1: Protein Unspecific Peroxygenase / Heme haloperoxidase family profile domain-containing protein


Mass: 30589.080 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Daldinia childiae (fungus) / Production host: Escherichia coli (E. coli) / References: unspecific peroxygenase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% (w/v) PEG 6000; 0.2 M CaCl2 dihydrate; 0.1 M MES pH 6.0

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.88→40.67 Å / Num. obs: 31736 / % possible obs: 99.7 % / Redundancy: 7 % / Biso Wilson estimate: 21 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.08 / Net I/σ(I): 7.4
Reflection shellResolution: 1.88→1.92 Å / Rmerge(I) obs: 1.18 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2030 / CC1/2: 0.69 / Rpim(I) all: 0.72

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Processing

Software
NameVersionClassification
REFMAC5.8.0431refinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→40.67 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.224 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26234 1612 5.1 %RANDOM
Rwork0.20461 ---
obs0.20743 30097 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.275 Å2
Baniso -1Baniso -2Baniso -3
1--3.15 Å2-0 Å21.37 Å2
2---2.92 Å2-0 Å2
3---5.73 Å2
Refinement stepCycle: 1 / Resolution: 1.88→40.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3294 0 89 189 3572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123479
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163081
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.8584768
X-RAY DIFFRACTIONr_angle_other_deg0.5941.7287096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1465431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.89532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.58210502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0820.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024159
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02777
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_it3.1523.5241730
X-RAY DIFFRACTIONr_mcbond_other3.1523.5251730
X-RAY DIFFRACTIONr_mcangle_it4.4226.3232159
X-RAY DIFFRACTIONr_mcangle_other4.4216.3242160
X-RAY DIFFRACTIONr_scbond_it3.5523.7191749
X-RAY DIFFRACTIONr_scbond_other3.5533.721748
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1336.7472610
X-RAY DIFFRACTIONr_long_range_B_refined6.94535.024094
X-RAY DIFFRACTIONr_long_range_B_other6.83634.94071
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 128 -
Rwork0.375 2184 -
obs--99.7 %

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