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- PDB-8rie: Crystallographic structure of oligosaccharide dehydrogenase from ... -

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Basic information

Entry
Database: PDB / ID: 8rie
TitleCrystallographic structure of oligosaccharide dehydrogenase from Pycnoporus cinnabarinus bound to Guaiacol, orthorhombic crystal
ComponentsGlucose oxidase
KeywordsOXIDOREDUCTASE / Oligosaccharide dehydrogenase / Pycnoporus cinnabarinus / Lignocellulose degradation / Sinapic Acid
Function / homology
Function and homology information


oxidoreductase activity, acting on CH-OH group of donors / flavin adenine dinucleotide binding
Similarity search - Function
Glucose Oxidase, domain 2 / GMC oxidoreductases signature 1. / 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 superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Guaiacol / Glucose oxidase
Similarity search - Component
Biological speciesTrametes cinnabarina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsSavino, C. / Sciara, G. / Gugole, E. / Vallone, B. / Fata, F. / Bulfaro, G. / Costanzo, A. / Montemiglio, L.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Towards an understanding of microbial lignin breakdown: fungal flavoenzymes prevent laccase-mediated polymerization of phenolic compounds
Authors: Savino, C. / Sciara, G. / Gugole, E. / Vallone, B. / Fata, F. / Bulfaro, G. / Costanzo, A. / Montemiglio, L.C. / Record, E.
History
DepositionDec 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 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 oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,48614
Polymers62,5611
Non-polymers2,92513
Water10,251569
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-51 kcal/mol
Surface area20710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.891, 61.530, 195.206
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 Glucose oxidase


Mass: 62560.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trametes cinnabarina (fungus) / Gene: BN946_scf184803.g17 / Production host: Aspergillus niger (mold) / References: UniProt: A0A060SC37

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Sugars , 2 types, 3 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}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.: 2 / 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 , 4 types, 579 molecules

#3: 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
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-JZ3 / Guaiacol / 2-methoxyphenol


Mass: 124.137 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H8O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 569 / 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: 2.37 Å3/Da / Density % sol: 48.12 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 2 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.291→97.62 Å / Num. obs: 57542 / % possible obs: 94.5 % / Redundancy: 12.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.081 / Net I/σ(I): 13.4
Reflection shellResolution: 1.291→1.426 Å / Rmerge(I) obs: 1.364 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4609 / CC1/2: 0.587

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→97.62 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.974 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21864 2843 5 %RANDOM
Rwork0.16751 ---
obs0.17003 54200 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.536 Å2
Baniso -1Baniso -2Baniso -3
1--2.39 Å2-0 Å20 Å2
2--0.91 Å2-0 Å2
3---1.48 Å2
Refinement stepCycle: 1 / Resolution: 1.78→97.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4410 0 188 569 5167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0135290
X-RAY DIFFRACTIONr_bond_other_d0.0040.0174897
X-RAY DIFFRACTIONr_angle_refined_deg1.691.6577346
X-RAY DIFFRACTIONr_angle_other_deg1.3871.59811389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4895743
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.18224.372247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.50215834
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4231517
X-RAY DIFFRACTIONr_chiral_restr0.0850.2733
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026248
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021206
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_it0.5860.4542556
X-RAY DIFFRACTIONr_mcbond_other0.5850.7372555
X-RAY DIFFRACTIONr_mcangle_it0.8760.6833236
X-RAY DIFFRACTIONr_mcangle_other0.8772.6513237
X-RAY DIFFRACTIONr_scbond_it1.0782734
X-RAY DIFFRACTIONr_scbond_other1.0782735
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3024034
X-RAY DIFFRACTIONr_long_range_B_refined2.256295
X-RAY DIFFRACTIONr_long_range_B_other1.4936108
X-RAY DIFFRACTIONr_rigid_bond_restr8.46235155
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 185 -
Rwork0.236 3645 -
obs--90.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.23980.29370.23440.84850.47021.54640.0695-1.1676-0.35680.3022-0.053-0.01590.32620.0162-0.01640.33380.0019-0.01450.60950.09980.0454-15.745-16.388833.949
23.2961-0.0847-0.06880.51150.43971.02640.0307-0.5260.0139-0.00750.0399-0.08730.04980.0971-0.07060.21120.0034-0.00610.1031-0.00860.024-9.6617-10.791515.2007
32.6922-0.0180.53020.88070.23431.21980.0365-0.8232-0.1170.13260.0094-0.04860.1708-0.0414-0.04590.24250.0043-00.26540.03560.0374-14.4317-13.211324.1672
42.88370.02850.70520.98050.2821.9278-0.0546-0.75690.9299-0.0135-0.0136-0.0284-0.15960.01490.06820.215-0.010.02520.223-0.26250.3184-10.31364.840219.6066
53.4528-0.40270.60210.9044-0.03712.12270.0624-0.7381.0737-0.07680.11090.0553-0.2893-0.0406-0.17340.2731-0.02650.02670.1649-0.24640.4555-18.33369.866517.9353
63.00261.0470.50691.1820.44382.24280.0886-1.29250.14790.1342-0.0842-0.18910.2029-0.0252-0.00440.20430.0212-0.03170.7161-0.16780.0793-0.8902-9.320626.1389
70.90760.23041.08931.0860.1091.3409-0.0537-0.39260.14990.1312-0.12920.0196-0.0678-0.42820.18290.23830.0173-0.00420.5391-0.08810.0269-15.5444-7.315927.8692
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 78
2X-RAY DIFFRACTION2A79 - 164
3X-RAY DIFFRACTION3A165 - 282
4X-RAY DIFFRACTION4A283 - 431
5X-RAY DIFFRACTION5A432 - 540
6X-RAY DIFFRACTION6A541 - 591
7X-RAY DIFFRACTION7A601

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