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- PDB-6xuv: Crystallographic structure of oligosaccharide dehydrogenase from ... -

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Basic information

Entry
Database: PDB / ID: 6xuv
TitleCrystallographic structure of oligosaccharide dehydrogenase from Pycnoporus cinnabarinus, laminaribiose-bound form
ComponentsOligosaccharide dehydrogenase
KeywordsOXIDOREDUCTASE / Glucose dehydrogenase / Pycnoporus cinnabarinus / Laminaribiose / oligosaccharide dehydrogenase
Function / homology
Function and homology information


oxidoreductase activity, acting on CH-OH group of donors / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / 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
beta-laminaribiose / FLAVIN-ADENINE DINUCLEOTIDE / alpha-D-glucopyranose / Glucose oxidase
Similarity search - Component
Biological speciesTrametes cinnabarina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 Å
AuthorsCerutti, G. / Savino, C. / Montemiglio, L.C. / Vallone, B. / Sciara, G.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR 19-CE43-0007 France
French National Institute of Agricultural Research (INRAE)ANS 2018-2019 France
CitationJournal: Biotechnol Biofuels / Year: 2021
Title: Crystal structure and functional characterization of an oligosaccharide dehydrogenase from Pycnoporus cinnabarinus provides insights into fungal breakdown of lignocellulose.
Authors: Cerutti, G. / Gugole, E. / Montemiglio, L.C. / Turbe-Doan, A. / Chena, D. / Navarro, D. / Lomascolo, A. / Piumi, F. / Exertier, C. / Freda, I. / Vallone, B. / Record, E. / Savino, C. / Sciara, G.
History
DepositionJan 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oligosaccharide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,25413
Polymers62,5611
Non-polymers3,69312
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint9 kcal/mol
Surface area19820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.914, 60.929, 194.286
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 Oligosaccharide dehydrogenase


Mass: 62560.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trametes cinnabarina (fungus) / Production host: Aspergillus niger (mold) / References: UniProt: A0A060SC37, EC: 1.1.5.9

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Sugars , 4 types, 8 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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose / beta-laminaribiose


Type: oligosaccharide, Oligosaccharide / Class: Antimicrobial / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-laminaribiose
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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 , 3 types, 306 molecules

#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / 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
#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.84 %
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: Diamond / Beamline: I24 / Wavelength: 0.9685 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9685 Å / Relative weight: 1
ReflectionResolution: 1.75→97.33 Å / Num. obs: 59350 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 0.99 / Net I/σ(I): 7
Reflection shellResolution: 1.75→2.02 Å / Num. unique obs: 20470 / CC1/2: 0.81

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.75→97.33 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / SU B: 11.205 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.117 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20729 3022 5.1 %RANDOM
Rwork0.16777 ---
obs0.16977 56520 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.779 Å2
Baniso -1Baniso -2Baniso -3
1--2.74 Å20 Å20 Å2
2--3.9 Å20 Å2
3----1.16 Å2
Refinement stepCycle: 1 / Resolution: 1.75→97.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4399 0 242 302 4943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0135570
X-RAY DIFFRACTIONr_bond_other_d0.0030.0174970
X-RAY DIFFRACTIONr_angle_refined_deg2.0051.6927766
X-RAY DIFFRACTIONr_angle_other_deg1.4361.6211733
X-RAY DIFFRACTIONr_dihedral_angle_1_deg16.8165.376797
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97824.038260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.93815849
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.051518
X-RAY DIFFRACTIONr_chiral_restr0.0980.2807
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027121
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021130
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_it1.5692.7992621
X-RAY DIFFRACTIONr_mcbond_other1.5682.7982620
X-RAY DIFFRACTIONr_mcangle_it2.1994.1933329
X-RAY DIFFRACTIONr_mcangle_other2.24.1933330
X-RAY DIFFRACTIONr_scbond_it1.9763.1182949
X-RAY DIFFRACTIONr_scbond_other1.8953.0872937
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8294.5754328
X-RAY DIFFRACTIONr_long_range_B_refined5.39333.8546192
X-RAY DIFFRACTIONr_long_range_B_other5.21733.1696108
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 216 -
Rwork0.432 4042 -
obs--98.93 %
Refinement TLS params.Method: refined / Origin x: -12.6317 Å / Origin y: 4.1841 Å / Origin z: -21.8624 Å
111213212223313233
T0.0056 Å2-0.0071 Å20.0085 Å2-0.1754 Å2-0.0667 Å2--0.0366 Å2
L2.6521 °2-0.1263 °2-0.1622 °2-0.8476 °20.2617 °2--0.9498 °2
S-0.0094 Å °0.6315 Å °-0.2468 Å °0.0047 Å °0.0066 Å °-0.0341 Å °-0.0031 Å °0.0862 Å °0.0028 Å °

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