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

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Basic information

Entry
Database: PDB / ID: 8rid
TitleCrystallographic structure of oligosaccharide dehydrogenase from Pycnoporus cinnabarinus bound to Sinapic Acid, 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 / SINAPINATE / Glucose oxidase
Similarity search - Component
Biological speciesTrametes cinnabarina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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)65,56213
Polymers62,5611
Non-polymers3,00112
Water11,980665
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.060, 61.883, 195.597
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
#5: 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, 674 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
#4: Chemical ChemComp-SXX / SINAPINATE


Mass: 224.210 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 665 / 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: 1.19→97.99 Å / Num. obs: 129361 / % possible obs: 95.6 % / Redundancy: 12.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Net I/σ(I): 14
Reflection shellResolution: 1.19→1.297 Å / Rmerge(I) obs: 1.119 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 6468 / CC1/2: 0.702

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→97.99 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.976 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17824 6054 4.9 %RANDOM
Rwork0.14251 ---
obs0.1443 116481 83.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.177 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å2-0 Å2-0 Å2
2---2.46 Å20 Å2
3---1.16 Å2
Refinement stepCycle: 1 / Resolution: 1.3→97.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4410 0 193 665 5268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0135273
X-RAY DIFFRACTIONr_bond_other_d0.0060.0174873
X-RAY DIFFRACTIONr_angle_refined_deg1.7461.6567312
X-RAY DIFFRACTIONr_angle_other_deg1.4861.59811335
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2475739
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.59224.198243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.80215828
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5061517
X-RAY DIFFRACTIONr_chiral_restr0.0960.2731
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026213
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021185
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_it1.180.9422563
X-RAY DIFFRACTIONr_mcbond_other1.1670.9412562
X-RAY DIFFRACTIONr_mcangle_it1.5861.4243240
X-RAY DIFFRACTIONr_mcangle_other1.5871.4253241
X-RAY DIFFRACTIONr_scbond_it1.7161.1462710
X-RAY DIFFRACTIONr_scbond_other1.7151.1472711
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.151.6694002
X-RAY DIFFRACTIONr_long_range_B_refined3.35313.6736216
X-RAY DIFFRACTIONr_long_range_B_other3.12812.4996015
X-RAY DIFFRACTIONr_rigid_bond_restr7.104310146
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 224 -
Rwork0.224 4135 -
obs--40.42 %
Refinement TLS params.Method: refined / Origin x: -12.3442 Å / Origin y: -4.0146 Å / Origin z: 22.0798 Å
111213212223313233
T0.005 Å20.0146 Å2-0.0066 Å2-0.1958 Å2-0.1034 Å2--0.0549 Å2
L2.6451 °20.0694 °20.191 °2-0.551 °20.0994 °2--0.7759 °2
S-0.0283 Å °-0.692 Å °0.3705 Å °0.0468 Å °0.0381 Å °-0.0074 Å °0.0174 Å °0.0182 Å °-0.0098 Å °

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