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- PDB-9rg2: Unspecific peroxygenase from Psathyrella aberdarensis, Grogu vari... -

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Basic information

Entry
Database: PDB / ID: 9rg2
TitleUnspecific peroxygenase from Psathyrella aberdarensis, Grogu variant, in complex with alpha-damascone
ComponentsHeme-thiolate peroxidase
KeywordsOXIDOREDUCTASE / Peroxygenase / peroxidase / complex / alpha-damascone
Function / homology
Function and homology information


unspecific peroxygenase / peroxidase activity / metal ion binding
Similarity search - Function
Chloroperoxidase / Chloroperoxidase-like superfamily / Peroxidase, family 2 / Heme haloperoxidase family profile.
Similarity search - Domain/homology
: / ETHANOL / PROTOPORPHYRIN IX CONTAINING FE / 2-acetamido-2-deoxy-alpha-D-glucopyranose / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Heme-thiolate peroxidase
Similarity search - Component
Biological speciesCandolleomyces aberdarensis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFernandez-Garcia, A. / Sanz-Aparicio, J.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesY2018/BIO-4738-EVOQUIMERA-CM Spain
Spanish Ministry of Science, Innovation, and UniversitiesPID2019-105838RB-C33 Spain
CitationJournal: Adv.Synth.Catal. / Year: 2026
Title: Structural features and reaction profile of an evolved unspecific peroxygenase from Candolleomyces aberdarensis
Authors: Fernandez-Garcia, A. / Sanz-Aparicio, J.
History
DepositionJun 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 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: Heme-thiolate peroxidase
B: Heme-thiolate peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,98647
Polymers73,1512
Non-polymers6,83545
Water15,367853
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: PISA-Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11640 Å2
ΔGint-424 kcal/mol
Surface area27300 Å2
Unit cell
Length a, b, c (Å)76.330, 76.330, 272.231
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Heme-thiolate peroxidase


Mass: 36575.500 Da / Num. of mol.: 2 / Mutation: S61A, L79I, A252L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candolleomyces aberdarensis (fungus) / Gene: EST38_g7491 / Production host: Komagataella phaffii CBS 7435 (fungus) / References: UniProt: A0A4Q2DF39, unspecific peroxygenase

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Sugars , 3 types, 11 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#8: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 10 types, 887 molecules

#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: 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
#7: Chemical ChemComp-A1IUA / alpha-damascone / (~{E})-1-(2,6,6-trimethylcyclohex-2-en-1-yl)but-2-en-1-one


Mass: 192.297 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H20O / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O
#12: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#13: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 853 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.05 Å3/Da / Density % sol: 59.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 11% (v/v) PEG 8000, 100mM MES pH 6.5, 150mM Zn chloride Cocrystallization 45mM alpha-damascone (incubation time: 35 minutes)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 14, 2023 / Details: KB MIRRORS
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→47.46 Å / Num. obs: 83156 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.027 / Rrim(I) all: 0.072 / Χ2: 0.8 / Net I/σ(I): 16.7
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 4497 / CC1/2: 0.853 / Rpim(I) all: 0.254 / Rrim(I) all: 0.665 / Χ2: 0.73 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→47.46 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.419 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18532 4074 4.9 %RANDOM
Rwork0.15468 ---
obs0.15615 78961 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.738 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20.15 Å20 Å2
2--0.3 Å2-0 Å2
3----0.97 Å2
Refinement stepCycle: 1 / Resolution: 1.8→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5364 0 208 853 6425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125777
X-RAY DIFFRACTIONr_bond_other_d0.0070.0165161
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.8367918
X-RAY DIFFRACTIONr_angle_other_deg0.6391.74711908
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3415690
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.134527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51410764
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0820.2859
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026801
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021387
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_it1.8082.3032694
X-RAY DIFFRACTIONr_mcbond_other1.8072.3032694
X-RAY DIFFRACTIONr_mcangle_it2.5444.133370
X-RAY DIFFRACTIONr_mcangle_other2.5444.133371
X-RAY DIFFRACTIONr_scbond_it2.9022.7413083
X-RAY DIFFRACTIONr_scbond_other2.8872.7333072
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3784.8794519
X-RAY DIFFRACTIONr_long_range_B_refined5.69725.296951
X-RAY DIFFRACTIONr_long_range_B_other5.69925.286946
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.843 Å
RfactorNum. reflection% reflection
Rfree0.249 259 -
Rwork0.219 5827 -
obs--98.88 %

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