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- PDB-9rg4: Unspecific peroxygenase from Psathyrella aberdarensis, Grogu vari... -

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Basic information

Entry
Database: PDB / ID: 9rg4
TitleUnspecific peroxygenase from Psathyrella aberdarensis, Grogu variant, in complex with 5-formyl-2-furoic acid
ComponentsHeme-thiolate peroxidase
KeywordsOXIDOREDUCTASE / Peroxygenase / peroxidase / complex / 5-formyl-2-furoic acid
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
: / beta-D-mannopyranose / ETHANOL / Mesoheme / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Heme-thiolate peroxidase
Similarity search - Component
Biological speciesCandolleomyces aberdarensis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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: To Be Published
Title: Unspecific peroxygenase from Psathyrella 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)80,22851
Polymers73,1512
Non-polymers7,07749
Water17,475970
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: PISA-monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12000 Å2
ΔGint-429 kcal/mol
Surface area28060 Å2
Unit cell
Length a, b, c (Å)76.496, 76.496, 273.210
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
#3: 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
#13: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 10 types, 1008 molecules

#4: 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
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O
#8: Chemical ChemComp-MH0 / Mesoheme


Mass: 620.519 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H36FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#12: Chemical ChemComp-A1JHS / 5-Formyl-2-furancarboxylic Acid / 5-methanoylfuran-2-carboxylic acid / 5-Formyl-2-furoic Acid


Mass: 140.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H4O4 / Feature type: SUBJECT OF INVESTIGATION
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 970 / 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: 3.07 Å3/Da / Density % sol: 59.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 14% (v/v) PEG 8000, 100mM MES pH 6.5, 150mM Zn chloride Cocrystallization 40mM 5-formyl-2-furoic acid (incubation time: 55 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: Nov 24, 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: 1.7→47.6 Å / Num. obs: 97778 / % possible obs: 98.5 % / Redundancy: 8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.023 / Rrim(I) all: 0.067 / Χ2: 0.8 / Net I/σ(I): 17.7
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4687 / CC1/2: 0.814 / Rpim(I) all: 0.297 / Rrim(I) all: 0.85 / Χ2: 0.73 / % possible all: 96.1

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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: 1.7→47.6 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.908 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17973 4772 4.9 %RANDOM
Rwork0.15257 ---
obs0.15387 93003 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.253 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20.17 Å20 Å2
2--0.34 Å20 Å2
3----1.1 Å2
Refinement stepCycle: 1 / Resolution: 1.7→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5370 0 217 970 6557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125785
X-RAY DIFFRACTIONr_bond_other_d0.0020.0165148
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.8357912
X-RAY DIFFRACTIONr_angle_other_deg0.5741.73911882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3845686
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.436528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52710764
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0730.2858
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026760
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021386
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_it1.5822.2732690
X-RAY DIFFRACTIONr_mcbond_other1.5822.2732690
X-RAY DIFFRACTIONr_mcangle_it2.2884.0783364
X-RAY DIFFRACTIONr_mcangle_other2.294.083365
X-RAY DIFFRACTIONr_scbond_it2.6622.7013095
X-RAY DIFFRACTIONr_scbond_other2.652.6963088
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0254.8114527
X-RAY DIFFRACTIONr_long_range_B_refined5.28825.267013
X-RAY DIFFRACTIONr_long_range_B_other5.28725.267014
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.741 Å
RfactorNum. reflection% reflection
Rfree0.235 347 -
Rwork0.223 6759 -
obs--96.89 %

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