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- PDB-7o1r: Unspecific peroxygenase from Hypoxylon sp. EC38 in complex with i... -

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Basic information

Entry
Database: PDB / ID: 7o1r
TitleUnspecific peroxygenase from Hypoxylon sp. EC38 in complex with imidazole
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
1,4-BUTANEDIOL / PROTOPORPHYRIN IX CONTAINING FE / IMIDAZOLE / DI(HYDROXYETHYL)ETHER / Cloroperoxidase
Similarity search - Component
Biological speciesHypoxylon sp. EC38 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: 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)29,98510
Polymers28,4621
Non-polymers1,5249
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-16 kcal/mol
Surface area10150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.726, 71.726, 153.704
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-499-

HOH

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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
#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.: 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 , 6 types, 229 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 222 / 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: 3.47 Å3/Da / Density % sol: 64.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG500 MME, 10% PEG20000, 0.1 M MES monohydrate pH 6.5, 0.1 M Imidazole

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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: Oct 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→48.21 Å / Num. obs: 99264 / % possible obs: 100 % / Redundancy: 25.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.032 / Rrim(I) all: 0.161 / Net I/σ(I): 14.8
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
1.3-1.3224.94.77112042348370.4430.9734.870.8100
7.12-48.1621.30.053158317430.9990.0120.05566.799.8

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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: MOLECULAR REPLACEMENT
Starting model: 5FUK

5fuk


Resolution: 1.3→48.21 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.529 / SU ML: 0.026 / SU R Cruickshank DPI: 0.0306 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.031 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1582 3000 3 %RANDOM
Rwork0.1398 ---
obs0.1404 96147 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.26 Å2 / Biso mean: 17.582 Å2 / Biso min: 6.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2---0.2 Å20 Å2
3---0.4 Å2
Refinement stepCycle: final / Resolution: 1.3→48.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1757 0 99 222 2078
Biso mean--24.05 29.11 -
Num. residues----227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0131980
X-RAY DIFFRACTIONr_bond_other_d0.0040.0171742
X-RAY DIFFRACTIONr_angle_refined_deg2.2861.7042706
X-RAY DIFFRACTIONr_angle_other_deg1.7111.624061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9285242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.36423.93999
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.06615290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.162158
X-RAY DIFFRACTIONr_chiral_restr0.1250.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022270
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02418
X-RAY DIFFRACTIONr_rigid_bond_restr7.82733720
LS refinement shellResolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 208 -
Rwork0.302 7028 -
all-7236 -
obs--100 %

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