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- PDB-7o1z: Unspecific peroxygenase from Hypoxylon sp. EC38 in complex with S... -

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Basic information

Entry
Database: PDB / ID: 7o1z
TitleUnspecific peroxygenase from Hypoxylon sp. EC38 in complex with S-1,2-propanediol
ComponentsPeroxygenase
KeywordsOXIDOREDUCTASE / peroxygenase / heme
Function / homology
Function and homology information


peroxidase activity / metal ion binding
Similarity search - Function
Chloroperoxidase / Chloroperoxidase-like / Chloroperoxidase / Chloroperoxidase-like superfamily / Peroxidase, family 2 / Heme haloperoxidase family profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1-BUTANOL / PROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER / S-1,2-PROPANEDIOL / Cloroperoxidase
Similarity search - Component
Biological speciesHypoxylon sp. EC38 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsRotilio, L. / Mattevi, A.
CitationJournal: Acs Catalysis / Year: 2021
Title: Structural and biochemical studies enlighten the unspecific peroxygenase from Hypoxylon sp. EC38 as an efficient oxidative biocatalyst.
Authors: Rotilio, L. / Swoboda, A. / Ebner, K. / Rinnofner, C. / Glieder, A. / Kroutil, W. / Mattevi, A.
History
DepositionMar 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,03910
Polymers28,4621
Non-polymers1,5779
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-14 kcal/mol
Surface area10100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.468, 71.468, 152.655
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein Peroxygenase / Cloroperoxidase / Peroxygenase


Mass: 28461.662 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypoxylon sp. EC38 (fungus) / Gene: K449DRAFT_467810 / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A1Y2TH07, unspecific peroxygenase
#4: 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.: 2 / 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

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Non-polymers , 7 types, 202 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-1BO / 1-BUTANOL / BUTAN-1-OL


Mass: 74.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O
#7: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 3.42 Å3/Da / Density % sol: 64.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG500 MME, 10% PEG20000, 0.1 M MES monohydrate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→48.02 Å / Num. obs: 37610 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.018 / Rrim(I) all: 0.063 / Net I/σ(I): 25.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.8412.80.4162818821960.9610.120.4345.8100
9-47.9810.70.04340953840.9970.0130.04556.899.5

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→48.02 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.236 / SU ML: 0.045 / SU R Cruickshank DPI: 0.0774 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1678 1138 3 %RANDOM
Rwork0.1226 ---
obs0.124 36394 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.01 Å2 / Biso mean: 24.589 Å2 / Biso min: 11.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20 Å2
2--0.87 Å20 Å2
3----1.73 Å2
Refinement stepCycle: final / Resolution: 1.8→48.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1737 0 105 195 2037
Biso mean--38.96 34.14 -
Num. residues----225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131974
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171752
X-RAY DIFFRACTIONr_angle_refined_deg2.0111.7052705
X-RAY DIFFRACTIONr_angle_other_deg1.5731.6124092
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0765243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.94224.22797
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47815288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.888157
X-RAY DIFFRACTIONr_chiral_restr0.0950.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022238
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02403
X-RAY DIFFRACTIONr_rigid_bond_restr4.05533725
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.183 84 -
Rwork0.125 2613 -
all-2697 -
obs--99.85 %

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