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- PDB-5oc1: Crystal structure of aryl-alcohol oxidase from Pleurotus eryngii ... -

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Basic information

Entry
Database: PDB / ID: 5oc1
TitleCrystal structure of aryl-alcohol oxidase from Pleurotus eryngii in complex with p-anisic acid
ComponentsAryl-alcohol oxidase
KeywordsOXIDOREDUCTASE / AAO / LIGNIN DEGRADATION / PLEUROTUS ERYNGII / FLAVOPROTEIN
Function / homology
Function and homology information


aryl-alcohol oxidase / aryl-alcohol oxidase activity / flavin adenine dinucleotide binding
Similarity search - Function
Glucose Oxidase; domain 3 / Glucose Oxidase, domain 3 / GMC oxidoreductases signature 2. / Glucose-methanol-choline oxidoreductase / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain ...Glucose Oxidase; domain 3 / Glucose Oxidase, domain 3 / GMC oxidoreductases signature 2. / Glucose-methanol-choline oxidoreductase / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
4-METHOXYBENZOIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / Aryl-alcohol oxidase
Similarity search - Component
Biological speciesPleurotus eryngii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCarro, J. / Martinez-Julvez, M. / Medina, M. / Martinez, A. / Ferreira, P.
Funding support Spain, 2items
OrganizationGrant numberCountry
MINEICOBIO2016-75183-P Spain
MINECOBIO2014-56388-R Spain
Citation
Journal: Phys Chem Chem Phys / Year: 2017
Title: Protein dynamics promote hydride tunnelling in substrate oxidation by aryl-alcohol oxidase.
Authors: Carro, J. / Martinez-Julvez, M. / Medina, M. / Martinez, A.T. / Ferreira, P.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2009
Title: Novel structural features in the GMC family of oxidoreductases revealed by the crystal structure of fungal aryl-alcohol oxidase.
Authors: Fernandez, I.S. / Duenas, F.J.R. / Santillana, E. / Ferreira, P. / Martinez, M.J. / Martinez, A.T. / Romero, A.
History
DepositionJun 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aryl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3308
Polymers60,9321
Non-polymers1,3987
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-4 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.326, 179.326, 160.177
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Aryl-alcohol oxidase


Mass: 60931.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pleurotus eryngii (fungus) / Gene: aao / Plasmid: PFLAG1 / Production host: Escherichia coli (E. coli) / References: UniProt: O94219, aryl-alcohol oxidase
#2: Chemical ChemComp-ANN / 4-METHOXYBENZOIC ACID / P-ANISIC ACID


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
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

Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M sodium acetate, pH 4.5 and 1.0 M di-ammonium hydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 2.3→43.99 Å / Num. obs: 67615 / % possible obs: 100 % / Redundancy: 40.1 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 28.1
Reflection shellResolution: 2.3→2.42 Å / Num. unique obs: 9716 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3fim

3fim


Resolution: 2.3→42.3 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.558 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.126 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19496 4896 7.2 %RANDOM
Rwork0.17431 ---
obs0.17583 62672 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.931 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å2-0.32 Å2-0 Å2
2---0.63 Å20 Å2
3---2.06 Å2
Refinement stepCycle: 1 / Resolution: 2.3→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4298 0 94 280 4672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194502
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.9666158
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5555564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77924.505202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97715643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9771526
X-RAY DIFFRACTIONr_chiral_restr0.1130.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213500
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.9083.1892259
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.0134.7752822
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5323.3382242
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.86627.1846947
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 359 -
Rwork0.24 4558 -
obs--100 %

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