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- PDB-8s2y: Crystal structure of alcohol oxidase PaAox1 from Picea abies -

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Basic information

Entry
Database: PDB / ID: 8s2y
TitleCrystal structure of alcohol oxidase PaAox1 from Picea abies
ComponentsGlucose-methanol-choline oxidoreductase N-terminal domain-containing protein
KeywordsOXIDOREDUCTASE / alcohol oxidase / FAD / flavin adenine dinucleotide / CAZyme
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE
Function and homology information
Biological speciesPicea abies (Norway spruce)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsKruhler, N. / Haataja, T. / Sandgren, M.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland331853 Finland
CitationJournal: To Be Published
Title: A glycerol oxidase from Norway spruce (Picea abies L. Karst.) expands biochemical and structural attributes of the GMC oxidoreductase superfamily
Authors: Paasela, T. / Kruhler, N. / Zhao, H. / Sun, M. / Haataja, T. / Karppi, J. / Vaattovaara, A. / Master, E. / Sandgren, M. / Karkonen, A. / Tenkanen, M.
History
DepositionFeb 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucose-methanol-choline oxidoreductase N-terminal domain-containing protein
B: Glucose-methanol-choline oxidoreductase N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,05820
Polymers143,8482
Non-polymers4,21118
Water13,763764
1
A: Glucose-methanol-choline oxidoreductase N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,10611
Polymers71,9241
Non-polymers2,18210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucose-methanol-choline oxidoreductase N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9539
Polymers71,9241
Non-polymers2,0298
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.099, 99.273, 87.959
Angle α, β, γ (deg.)90, 100.249, 90
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: ALA / End label comp-ID: ALA / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 29 - 546 / Label seq-ID: 118 - 635

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glucose-methanol-choline oxidoreductase N-terminal domain-containing protein


Mass: 71923.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: There are unobserved regions. / Source: (gene. exp.) Picea abies (Norway spruce) / Production host: Komagataella phaffii (fungus) / Strain (production host): X33

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Sugars , 2 types, 10 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: 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.: 9 / 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 , 5 types, 772 molecules

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


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 764 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.17 Å3/Da / Density % sol: 43.2 % / Description: Needle crystal
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M CaCl2 20% PEG 3350

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.64→65.24 Å / Num. obs: 123313 / % possible obs: 94.6 % / Redundancy: 6.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.05 / Net I/av σ(I): 1.06 / Net I/σ(I): 10.5
Reflection shellResolution: 1.64→1.67 Å / Num. unique obs: 13965 / CC1/2: 0.33 / Rrim(I) all: 1.802 / % possible all: 61.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→65.24 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.179 / WRfactor Rwork: 0.159 / SU B: 3.034 / SU ML: 0.091 / Average fsc free: 0.9422 / Average fsc work: 0.9475 / Cross valid method: FREE R-VALUE / ESU R: 0.101 / ESU R Free: 0.097 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2096 6243 5.078 %
Rwork0.1851 116690 -
all0.186 --
obs-122933 94.285 %
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: 29.154 Å2
Baniso -1Baniso -2Baniso -3
1--0.001 Å2-0 Å20.001 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.64→65.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7437 0 271 764 8472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0127982
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.8210875
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0415971
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.084565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.084101203
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.31810370
X-RAY DIFFRACTIONr_chiral_restr0.1320.21203
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026180
X-RAY DIFFRACTIONr_nbd_refined0.2020.23815
X-RAY DIFFRACTIONr_nbtor_refined0.3090.25417
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2712
X-RAY DIFFRACTIONr_metal_ion_refined0.0750.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1620.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1250.216
X-RAY DIFFRACTIONr_mcbond_it2.6352.5343869
X-RAY DIFFRACTIONr_mcangle_it3.6924.5284830
X-RAY DIFFRACTIONr_scbond_it4.1733.1024113
X-RAY DIFFRACTIONr_scangle_it6.2745.4946040
X-RAY DIFFRACTIONr_lrange_it7.49128.17312538
X-RAY DIFFRACTIONr_ncsr_local_group_10.0870.0515943
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.08660.05009
12AX-RAY DIFFRACTIONLocal ncs0.08660.05009
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
1.64-1.6830.4242960.41857040.41896500.7490.74962.17620.42
1.683-1.7290.3853350.39467200.39493480.8040.79675.47070.39
1.729-1.7790.3684080.36175750.36190960.8990.90387.76390.353
1.779-1.8330.3124390.30780390.30788380.9230.92795.92670.289
1.833-1.8940.2884150.25781900.25986060.9440.95399.98840.231
1.894-1.960.2594230.23178550.23382810.9520.96499.96380.203
1.96-2.0340.2484270.20675880.20880160.960.97299.98750.179
2.034-2.1170.2374020.19572770.19776790.9660.9761000.168
2.117-2.2110.2113520.17970620.1874140.9720.981000.155
2.211-2.3190.2093640.16867010.1770660.9720.98399.98580.147
2.319-2.4440.2063500.16963830.17167330.9740.9831000.145
2.444-2.5920.2013170.16260640.16463810.9760.9841000.14
2.592-2.770.1983170.16656710.16859880.9760.9831000.145
2.77-2.9920.2122890.17452760.17655650.9740.9811000.154
2.992-3.2770.1842590.16848990.16851590.9780.98399.98060.152
3.277-3.6630.1932280.16444490.16546770.9780.9851000.152
3.663-4.2270.1552110.13638790.13740900.9860.991000.128
4.227-5.1710.1451810.12633270.12735080.9890.9921000.122
5.171-7.2910.2091600.18725490.18827090.9820.9841000.179
7.291-65.240.184700.20814750.20715450.9860.9751000.212

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