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- PDB-9wa6: Unspecific peroxygenase from Daldinia sp. EC12 in complex with PG4 -

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Basic information

Entry
Database: PDB / ID: 9wa6
TitleUnspecific peroxygenase from Daldinia sp. EC12 in complex with PG4
ComponentsUnspecific peroxygenase
KeywordsOXIDOREDUCTASE / unspecific peroxygenase / UPO
Function / homologyPROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesDaldinia sp. EC12 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsKim, J.H. / Kim, J.W. / Kim, J.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2023-00219517 Korea, Republic Of
CitationJournal: To Be Published
Title: Unspecific peroxygenase from Daldinia sp. EC12 in complex with PG4
Authors: Kim, J.H. / Kim, J.W. / Kim, J.S.
History
DepositionAug 11, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,7968
Polymers50,1262
Non-polymers1,6706
Water14,052780
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-87 kcal/mol
Surface area19300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.236, 64.739, 162.054
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Unspecific peroxygenase


Mass: 25062.959 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Daldinia sp. EC12 (fungus) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 780 / 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

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES sodium (pH 7.5), 20% PEG 4000, 10% 2-Propanol, 0.1 mM 2-mercaptoethanol. Cryoprotected with 25% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.89→47.3 Å / Num. obs: 49119 / % possible obs: 98.96 % / Redundancy: 5.6 % / Rpim(I) all: 0.095 / Rsym value: 0.232 / Net I/σ(I): 6.9
Reflection shellResolution: 1.89→1.96 Å / Num. unique obs: 49111 / Rpim(I) all: 0.484 / Rsym value: 1.021

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FUK

5fuk


Resolution: 1.89→47.29 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.68 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2219 1966 4 %
Rwork0.1807 --
obs0.1824 49119 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.89→47.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3561 0 28 780 4369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063693
X-RAY DIFFRACTIONf_angle_d0.9555054
X-RAY DIFFRACTIONf_dihedral_angle_d12.014502
X-RAY DIFFRACTIONf_chiral_restr0.055532
X-RAY DIFFRACTIONf_plane_restr0.007655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.940.31531270.28333062X-RAY DIFFRACTION91
1.94-1.990.31671370.26653272X-RAY DIFFRACTION98
1.99-2.050.2921390.24453311X-RAY DIFFRACTION99
2.05-2.120.28281390.22473353X-RAY DIFFRACTION100
2.12-2.190.24421390.20663348X-RAY DIFFRACTION100
2.19-2.280.25421400.19323358X-RAY DIFFRACTION100
2.28-2.390.24721410.19073368X-RAY DIFFRACTION99
2.39-2.510.2521410.18513365X-RAY DIFFRACTION100
2.51-2.670.22221400.18593385X-RAY DIFFRACTION100
2.67-2.880.20181420.17493398X-RAY DIFFRACTION100
2.88-3.160.20591420.17083415X-RAY DIFFRACTION100
3.16-3.620.20241430.15823434X-RAY DIFFRACTION100
3.62-4.560.18831450.13763462X-RAY DIFFRACTION100
4.56-47.290.1791510.17023622X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 41.8761 Å / Origin y: 20.3372 Å / Origin z: 98.8859 Å
111213212223313233
T-0.0539 Å2-0.0598 Å2-0.141 Å2-0.0076 Å2-0.0619 Å2---0.0662 Å2
L0.0403 °2-0.0326 °20.1048 °2-0.0652 °2-0.0091 °2--0.0703 °2
S-0.0216 Å °-0.0276 Å °-0.0675 Å °0.1119 Å °0.0367 Å °-0.011 Å °0.039 Å °-0.0199 Å °0.0018 Å °
Refinement TLS groupSelection details: all

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