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- PDB-8rno: Unspecific peroxygenase from Marasmius wettsteinii (MweUPO-1) in ... -

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Basic information

Entry
Database: PDB / ID: 8rno
TitleUnspecific peroxygenase from Marasmius wettsteinii (MweUPO-1) in complex with isophorone
ComponentsUnspecific peroxygenase
KeywordsOXIDOREDUCTASE / Peroxygenase / peroxidase / complex / isophorone
Function / homology: / PROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesMarasmius wettsteinii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsFernandez-Garcia, A. / Sanz-Aparicio, J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesSynergy CAM Project Y2018/BIO-4738-EVOQUIMERA-CM Spain
CitationJournal: Acs Chem.Biol. / Year: 2024
Title: Structural Insights and Reaction Profile of a New Unspecific Peroxygenase from Marasmius wettsteinii Produced in a Tandem-Yeast Expression System.
Authors: Sanchez-Moreno, I. / Fernandez-Garcia, A. / Mateljak, I. / Gomez de Santos, P. / Hofrichter, M. / Kellner, H. / Sanz-Aparicio, J. / Alcalde, M.
History
DepositionJan 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)55,19422
Polymers51,7982
Non-polymers3,39620
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: PISA-dimeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-79 kcal/mol
Surface area20250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.233, 76.233, 185.484
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein / Sugars , 2 types, 6 molecules AB

#1: Protein Unspecific peroxygenase


Mass: 25899.092 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marasmius wettsteinii (fungus) / Production host: Komagataella phaffii CBS 7435 (fungus) / References: unspecific peroxygenase
#2: 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.: 4
Source method: isolated from a genetically manipulated source
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, 183 molecules

#3: 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
#4: Chemical ChemComp-A1H13 / 3,5,5-trimethylcyclohex-2-en-1-one / Isophorone


Mass: 138.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.45 Å3/Da / Density % sol: 49.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 12% PEG 4000, 200mM ammonium sulfate. Soaking: 30 mM isophorone, 16 hours, cryoprotected with 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 22, 2021 / Details: KB MIRRORS
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.05→48.07 Å / Num. obs: 33452 / % possible obs: 95.2 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.019 / Rrim(I) all: 0.055 / Χ2: 0.94 / Net I/σ(I): 16.4
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2627 / CC1/2: 0.922 / Rpim(I) all: 0.214 / Rrim(I) all: 0.602 / Χ2: 0.86 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→48.07 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.174 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24785 1678 5 %RANDOM
Rwork0.20156 ---
obs0.20396 31696 94.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.954 Å2
Baniso -1Baniso -2Baniso -3
1-2.48 Å20 Å2-0 Å2
2--2.48 Å20 Å2
3----4.96 Å2
Refinement stepCycle: 1 / Resolution: 2.05→48.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3853 0 12 167 4032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0124004
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163739
X-RAY DIFFRACTIONr_angle_refined_deg1.2941.6915477
X-RAY DIFFRACTIONr_angle_other_deg0.4431.5968629
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3575494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.994528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44310606
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0640.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024702
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02886
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_it4.2085.4471934
X-RAY DIFFRACTIONr_mcbond_other4.2085.4471934
X-RAY DIFFRACTIONr_mcangle_it5.5689.7832418
X-RAY DIFFRACTIONr_mcangle_other5.5679.7852419
X-RAY DIFFRACTIONr_scbond_it4.3745.8472070
X-RAY DIFFRACTIONr_scbond_other4.3465.8222063
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2510.5163040
X-RAY DIFFRACTIONr_long_range_B_refined7.90455.364613
X-RAY DIFFRACTIONr_long_range_B_other7.91455.414590
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 114 -
Rwork0.315 2370 -
obs--97.45 %

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