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- PDB-9h92: FAD-dependent oxidase sorD -

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Basic information

Entry
Database: PDB / ID: 9h92
TitleFAD-dependent oxidase sorD
ComponentsFAD-linked oxidoreductase sorD
KeywordsOXIDOREDUCTASE / Flavin / FAD / natural product / oxidase / sorbicillinoids
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / 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 / THIOCYANATE ION / FAD-linked oxidoreductase sorD
Similarity search - Component
Biological speciesPenicillium rubens Wisconsin 54-1255 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsTjallinks, G. / Mattevi, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Cooperation in Science and Technology (COST) actionCOZYME (CA21162)European Union
CitationJournal: Acs Chem.Biol. / Year: 2025
Title: Structural and Mechanistic Characterization of the Flavin-Dependent Monooxygenase and Oxidase Involved in Sorbicillinoid Biosynthesis.
Authors: Tjallinks, G. / Angeleri, N. / Nguyen, Q.T. / Mannucci, B. / Arentshorst, M. / Visser, J. / Ram, A.F.J. / Fraaije, M.W. / Mattevi, A.
History
DepositionOct 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FAD-linked oxidoreductase sorD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3288
Polymers50,4451
Non-polymers2,8847
Water10,881604
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint23 kcal/mol
Surface area18330 Å2
Unit cell
Length a, b, c (Å)65.115, 115.720, 137.426
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-656-

HOH

21A-790-

HOH

31A-830-

HOH

41A-1013-

HOH

51A-1042-

HOH

61A-1140-

HOH

71A-1161-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein FAD-linked oxidoreductase sorD / Sorbicillinoid biosynthetic cluster protein D


Mass: 50444.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium rubens Wisconsin 54-1255 (fungus)
Gene: sorD, Pc21g05110 / Production host: Aspergillus niger (mold)
References: UniProt: B6HNK6, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor

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Sugars , 3 types, 5 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-alpha-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
DManpa1-6DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: 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-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.: 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 , 3 types, 606 molecules

#4: 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
#6: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / 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: 2.57 Å3/Da / Density % sol: 52.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.2 M K thiocyanate, 20 % PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.55→137.43 Å / Num. obs: 75455 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.072 / Rrim(I) all: 0.186 / Χ2: 1.01 / Net I/σ(I): 6.9 / Num. measured all: 494466
Reflection shellResolution: 1.55→1.58 Å / % possible obs: 100 % / Redundancy: 5.7 % / Rmerge(I) obs: 1.586 / Num. measured all: 21068 / Num. unique obs: 3698 / CC1/2: 0.578 / Rpim(I) all: 0.726 / Rrim(I) all: 1.747 / Χ2: 1.01 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→68.71 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.011 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20161 3781 5 %RANDOM
Rwork0.1688 ---
obs0.1704 71628 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.007 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0 Å20 Å2
2--1.69 Å20 Å2
3----1.56 Å2
Refinement stepCycle: 1 / Resolution: 1.55→68.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3526 0 190 607 4323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123821
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163376
X-RAY DIFFRACTIONr_angle_refined_deg1.751.85233
X-RAY DIFFRACTIONr_angle_other_deg0.9171.727786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4555467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.935514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.22610518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1590.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024495
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02890
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_it1.2991.551867
X-RAY DIFFRACTIONr_mcbond_other1.2981.5481865
X-RAY DIFFRACTIONr_mcangle_it1.7632.7782330
X-RAY DIFFRACTIONr_mcangle_other1.7632.7792331
X-RAY DIFFRACTIONr_scbond_it2.8161.9481954
X-RAY DIFFRACTIONr_scbond_other2.7911.9481953
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2313.4392901
X-RAY DIFFRACTIONr_long_range_B_refined5.65619.644610
X-RAY DIFFRACTIONr_long_range_B_other5.32817.194411
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 284 -
Rwork0.31 5241 -
obs--99.98 %

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