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

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Basic information

Entry
Database: PDB / ID: 8rnp
TitleUnspecific peroxygenase from Marasmius wettsteinii (MweUPO-1) in complex with R-limonene
ComponentsUnspecific peroxygenase
KeywordsOXIDOREDUCTASE / Peroxygenase / peroxidase / complex / R-limonene
Function / homology(4R)-1-methyl-4-(prop-1-en-2-yl)cyclohex-1-ene / PROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesMarasmius wettsteinii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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)55,06221
Polymers51,7982
Non-polymers3,26419
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: PISA-dimeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-103 kcal/mol
Surface area20250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.010, 75.010, 186.085
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
#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.: 4 / 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, 231 molecules

#2: 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-9IR / (4R)-1-methyl-4-(prop-1-en-2-yl)cyclohex-1-ene / R-(+)-limonene


Mass: 136.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16 / Feature type: SUBJECT OF INVESTIGATION
#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.: 3 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 26% PEG 4000, 100mM sodium acetate pH 4.6, 200mM ammonium sulfate. Soaking: 20 mM R-limonene, 16 hours, cryoprotected with 20% 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: 1.92→47.85 Å / Num. obs: 39559 / % possible obs: 95.4 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.023 / Rrim(I) all: 0.067 / Net I/σ(I): 12.7
Reflection shellResolution: 1.92→1.96 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2581 / CC1/2: 0.923 / Rpim(I) all: 0.242 / Rrim(I) all: 0.675 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→47.85 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.601 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25618 1933 4.9 %RANDOM
Rwork0.19893 ---
obs0.20167 37551 94.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.522 Å2
Baniso -1Baniso -2Baniso -3
1-2.92 Å20 Å20 Å2
2--2.92 Å20 Å2
3----5.83 Å2
Refinement stepCycle: 1 / Resolution: 1.92→47.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3838 0 17 216 4071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0124003
X-RAY DIFFRACTIONr_bond_other_d0.0040.0163734
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.8435479
X-RAY DIFFRACTIONr_angle_other_deg0.5041.7768615
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0075498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.363528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.65610608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0630.2609
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024760
X-RAY DIFFRACTIONr_gen_planes_other0.010.02900
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_it3.4224.7371938
X-RAY DIFFRACTIONr_mcbond_other3.4214.7371938
X-RAY DIFFRACTIONr_mcangle_it4.7338.52424
X-RAY DIFFRACTIONr_mcangle_other4.7328.5032425
X-RAY DIFFRACTIONr_scbond_it3.7455.0922065
X-RAY DIFFRACTIONr_scbond_other3.6395.0642054
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4829.1493028
X-RAY DIFFRACTIONr_long_range_B_refined7.61946.344632
X-RAY DIFFRACTIONr_long_range_B_other7.62146.374603
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.968 Å
RfactorNum. reflection% reflection
Rfree0.37 143 -
Rwork0.357 2692 -
obs--94.15 %

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