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- PDB-9avh: Crystal structure of an aryl-alcohol-oxidase from Bjerkandera adusta. -

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Basic information

Entry
Database: PDB / ID: 9avh
TitleCrystal structure of an aryl-alcohol-oxidase from Bjerkandera adusta.
ComponentsAryl Alcohol Oxidase
KeywordsOXIDOREDUCTASE / AAO / BJERKANDERA ADUSTA / FLAVOPROTEIN
Function / homology4-METHOXYBENZOIC ACID / FLAVIN-ADENINE DINUCLEOTIDE
Function and homology information
Biological speciesBjerkandera adusta (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMartinez-Julvez, M. / Ferreira, P.
Funding support Spain, 2items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)TED2021-130803B-I00 Spain
Other governmentBiologia Estructural E35_23R
CitationJournal: Front Bioeng Biotechnol / Year: 2024
Title: Unveiling the kinetic versatility of aryl-alcohol oxidases with different electron acceptors.
Authors: Serrano, A. / Cinca-Fernando, P. / Carro, J. / Velazquez-Campoy, A. / Martinez-Julvez, M. / Martinez, A.T. / Ferreira, P.
History
DepositionMar 3, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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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)64,78314
Polymers62,8091
Non-polymers1,97513
Water6,593366
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-64 kcal/mol
Surface area20120 Å2
Unit cell
Length a, b, c (Å)56.035, 82.746, 116.837
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Aryl Alcohol Oxidase


Mass: 62808.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bjerkandera adusta (fungus) / Production host: Escherichia coli (E. coli) / References: aryl-alcohol oxidase

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Non-polymers , 5 types, 379 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-ANN / 4-METHOXYBENZOIC ACID / P-ANISIC ACID


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3 / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.16 Å3/Da / Density % sol: 42.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 12% v/v glycerol, 1.5 M ammonium sulfate, 0.1 mM Tris/HCl, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979257 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979257 Å / Relative weight: 1
ReflectionResolution: 1.8→116.84 Å / Num. obs: 50514 / % possible obs: 98.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 12.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.843 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 7207 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→67.526 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.532 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.11 / ESU R Free: 0.111
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1883 2464 4.883 %
Rwork0.1434 47994 -
all0.146 --
obs-50458 98.699 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.479 Å2
Baniso -1Baniso -2Baniso -3
1--0.296 Å2-0 Å20 Å2
2---1.286 Å2-0 Å2
3---1.582 Å2
Refinement stepCycle: LAST / Resolution: 1.8→67.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4407 0 124 366 4897
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124640
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164276
X-RAY DIFFRACTIONr_angle_refined_deg1.6651.8036345
X-RAY DIFFRACTIONr_angle_other_deg0.5691.7399850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6415579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.812527
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.037201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.67910693
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.55310195
X-RAY DIFFRACTIONr_chiral_restr0.0830.2722
X-RAY DIFFRACTIONr_chiral_restr_other0.0060.21
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025483
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021026
X-RAY DIFFRACTIONr_nbd_refined0.2180.2935
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.24168
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22351
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22354
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2294
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1960.215
X-RAY DIFFRACTIONr_nbd_other0.2530.261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1860.28
X-RAY DIFFRACTIONr_mcbond_it1.7812.1862316
X-RAY DIFFRACTIONr_mcbond_other1.782.1862316
X-RAY DIFFRACTIONr_mcangle_it2.4633.922895
X-RAY DIFFRACTIONr_mcangle_other2.4643.922896
X-RAY DIFFRACTIONr_scbond_it3.0392.5622324
X-RAY DIFFRACTIONr_scbond_other2.9952.5192301
X-RAY DIFFRACTIONr_scangle_it4.5624.543450
X-RAY DIFFRACTIONr_scangle_other4.4864.4623415
X-RAY DIFFRACTIONr_lrange_it7.41823.3245246
X-RAY DIFFRACTIONr_lrange_other7.32122.9245167
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.8-1.8470.241720.2234510.22136990.9570.96197.94540.196
1.847-1.8970.261770.20133970.20436480.9510.96997.97150.177
1.897-1.9520.2091830.18832700.18935250.970.97497.95740.161
1.952-2.0120.2111710.16232210.16434580.9720.98298.09140.139
2.012-2.0780.191740.15531260.15733540.9790.98398.390.133
2.078-2.1510.1911540.14329850.14631790.9770.98698.74170.124
2.151-2.2320.1861620.13729320.1431520.9770.98898.15990.12
2.232-2.3230.1671500.13128170.13330040.9810.98998.76830.115
2.323-2.4260.1981280.13227270.13528900.9770.98998.78890.115
2.426-2.5450.1741480.13125890.13327620.9810.9999.09490.115
2.545-2.6820.1891290.1324720.13326290.980.9998.9350.115
2.682-2.8450.191260.13723690.1425110.9790.98899.36280.123
2.845-3.0410.19920.13522390.13723460.9780.98899.36060.123
3.041-3.2840.166930.13321160.13522230.9830.98999.37020.126
3.284-3.5960.181910.13619300.13820350.9810.98999.3120.13
3.596-4.0190.163770.1317650.13218500.9850.9999.56760.129
4.019-4.6380.183930.11915540.12216540.9820.99299.57680.121
4.638-5.6740.18590.1413470.14214130.9810.9999.50460.141
5.674-7.9960.208520.1810590.18111200.9770.98599.19640.177
7.996-67.5260.198330.176290.1726720.980.98198.51190.172

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