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- PDB-8s6g: Carbohydrate active oxidoreductase from Alternaria alternata -

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Basic information

Entry
Database: PDB / ID: 8s6g
TitleCarbohydrate active oxidoreductase from Alternaria alternata
ComponentsFAD-binding domain-containing protein
KeywordsOXIDOREDUCTASE / AA7 / BBE-enzyme / pectin / Alternaria alternata / phytopathogen
Function / homology
Function and homology information


FAD binding / oxidoreductase activity
Similarity search - Function
: / Berberine/berberine-like / Berberine and berberine like / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / FAD-binding domain-containing protein
Similarity search - Component
Biological speciesAlternaria alternata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsBanerjee, S. / Turella, S. / Morth, J.P. / Abou Hachem, M.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF20OC0064747 Denmark
CitationJournal: Nat Commun / Year: 2025
Title: Enzymatic oxidation of galacturonides from pectin breakdown contributes to stealth infection by Oomycota phytopathogens.
Authors: Turella, S. / He, C. / Zhao, L. / Banerjee, S. / Plouhinec, L. / Assiah Yao, R. / Norgaard Kejlstrup, M.C. / Grisel, S. / So, Y. / Annic, B. / Fanuel, M. / Haddad Momeni, M. / Bissaro, B. / ...Authors: Turella, S. / He, C. / Zhao, L. / Banerjee, S. / Plouhinec, L. / Assiah Yao, R. / Norgaard Kejlstrup, M.C. / Grisel, S. / So, Y. / Annic, B. / Fanuel, M. / Haddad Momeni, M. / Bissaro, B. / Meier, S. / Morth, J.P. / Dong, S. / Berrin, J.G. / Abou Hachem, M.
History
DepositionFeb 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: Database references / Category: citation / citation_author
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FAD-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,67312
Polymers53,9971
Non-polymers2,67711
Water12,611700
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint9 kcal/mol
Surface area19040 Å2
Unit cell
Length a, b, c (Å)61.893, 69.541, 62.700
Angle α, β, γ (deg.)90.000, 93.966, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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Protein , 1 types, 1 molecules A

#1: Protein FAD-binding domain-containing protein


Mass: 53996.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alternaria alternata (fungus) / Gene: CC77DRAFT_598273 / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A177D2A1

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Sugars , 2 types, 4 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
#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.: 3 / 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 , 6 types, 707 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 700 / 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: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium HEPES pH 7.5, 20% w/v PEG 10K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.208→62.56 Å / Num. obs: 159342 / % possible obs: 98.3 % / Redundancy: 6.6 % / Biso Wilson estimate: 12.71 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.7
Reflection shellResolution: 1.208→1.23 Å / Num. unique obs: 8198 / CC1/2: 0.754

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.21→30.3 Å / SU ML: 0.1021 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.7643
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1842 7975 5.01 %
Rwork0.1623 151251 -
obs0.1634 159226 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.11 Å2
Refinement stepCycle: LAST / Resolution: 1.21→30.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3714 0 173 703 4590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00794096
X-RAY DIFFRACTIONf_angle_d1.19865605
X-RAY DIFFRACTIONf_chiral_restr0.0931615
X-RAY DIFFRACTIONf_plane_restr0.008711
X-RAY DIFFRACTIONf_dihedral_angle_d12.1485602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.220.22972090.21194280X-RAY DIFFRACTION83.63
1.22-1.240.22342540.20274635X-RAY DIFFRACTION90.34
1.24-1.250.20862590.19294875X-RAY DIFFRACTION95.8
1.25-1.270.18892770.17715053X-RAY DIFFRACTION98.98
1.27-1.280.21642730.17955092X-RAY DIFFRACTION99.28
1.28-1.30.21242300.17415088X-RAY DIFFRACTION99.36
1.3-1.320.21132470.17335110X-RAY DIFFRACTION99.26
1.32-1.340.20092470.16615131X-RAY DIFFRACTION99.19
1.34-1.360.19612610.15955024X-RAY DIFFRACTION99.25
1.36-1.380.17412340.15695101X-RAY DIFFRACTION98.92
1.38-1.410.20092500.1595068X-RAY DIFFRACTION98.74
1.41-1.430.19572400.15445113X-RAY DIFFRACTION98.91
1.43-1.460.17732750.1495063X-RAY DIFFRACTION99.18
1.46-1.490.1692590.14285046X-RAY DIFFRACTION98.75
1.49-1.520.16242530.14525061X-RAY DIFFRACTION98.48
1.52-1.560.17892680.1445110X-RAY DIFFRACTION99.52
1.56-1.60.16962690.14585084X-RAY DIFFRACTION99.57
1.6-1.640.17462940.15065091X-RAY DIFFRACTION99.28
1.64-1.690.1863060.15315059X-RAY DIFFRACTION99.32
1.69-1.740.18353430.15495017X-RAY DIFFRACTION99.35
1.74-1.80.20492610.15335079X-RAY DIFFRACTION99.27
1.8-1.880.16142730.15785107X-RAY DIFFRACTION99.21
1.88-1.960.19133100.16115044X-RAY DIFFRACTION98.91
1.96-2.070.1992670.16425019X-RAY DIFFRACTION97.89
2.07-2.190.17422640.16055110X-RAY DIFFRACTION99.67
2.19-2.360.17442420.16175174X-RAY DIFFRACTION99.78
2.36-2.60.17442560.16425181X-RAY DIFFRACTION99.76
2.6-2.980.19983140.17135080X-RAY DIFFRACTION99.54
2.98-3.750.18632810.16125110X-RAY DIFFRACTION98.65
3.75-30.30.17022590.16645246X-RAY DIFFRACTION99.14

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