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- PDB-9ffe: Carbohydrate active oxidoreductases from Phytophthora sojae -

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Basic information

Entry
Database: PDB / ID: 9ffe
TitleCarbohydrate active oxidoreductases from Phytophthora sojae
ComponentsFAD-binding PCMH-type domain-containing protein
KeywordsOXIDOREDUCTASE / AA7 / BBE-enzyme / pectin / Phytopathogen / Phytophthora sojae
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 / alpha-D-mannopyranose / OXYGEN MOLECULE / FAD-binding PCMH-type domain-containing protein
Similarity search - Component
Biological speciesPhytophthora sojae (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 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
DepositionMay 23, 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 PCMH-type domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7678
Polymers51,8841
Non-polymers1,8837
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.045, 50.500, 53.092
Angle α, β, γ (deg.)88.100, 68.130, 74.280
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

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Protein , 1 types, 1 molecules A

#1: Protein FAD-binding PCMH-type domain-containing protein


Mass: 51884.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phytophthora sojae (eukaryote) / Gene: PHYSODRAFT_474098, PHYSODRAFT_476693 / Production host: Komagataella pastoris (fungus) / References: UniProt: G4YQ65

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Sugars , 2 types, 5 molecules

#2: 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.: 4 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
#5: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 112 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-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 1.98 Å3/Da / Density % sol: 37.99 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 2.0 M Ammonium sulfate, 0.1 M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.12→38.42 Å / Num. obs: 22006 / % possible obs: 97.3 % / Redundancy: 6.6 % / Biso Wilson estimate: 32.08 Å2 / CC1/2: 0.987 / Net I/σ(I): 6
Reflection shellResolution: 2.12→2.18 Å / Num. unique obs: 1603 / CC1/2: 0.499

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→25.87 Å / SU ML: 0.2647 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.1325
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2261 1098 5.02 %
Rwork0.1737 20768 -
obs0.1762 21866 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.82 Å2
Refinement stepCycle: LAST / Resolution: 2.12→25.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3622 0 122 110 3854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00773850
X-RAY DIFFRACTIONf_angle_d0.89725239
X-RAY DIFFRACTIONf_chiral_restr0.0509582
X-RAY DIFFRACTIONf_plane_restr0.0071661
X-RAY DIFFRACTIONf_dihedral_angle_d7.9606547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.220.35371490.27552309X-RAY DIFFRACTION88.16
2.22-2.330.30261320.25232601X-RAY DIFFRACTION96.61
2.33-2.480.30121310.22922629X-RAY DIFFRACTION97.18
2.48-2.670.29551320.21972653X-RAY DIFFRACTION98.24
2.67-2.940.26241490.20472600X-RAY DIFFRACTION98.42
2.94-3.360.25031460.18792641X-RAY DIFFRACTION98.27
3.36-4.230.22071080.13532686X-RAY DIFFRACTION99.15
4.24-25.870.13651510.12742649X-RAY DIFFRACTION99.19

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