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- PDB-9h8z: FAD-dependent monooxygenase sorC with sorbicillin bound -

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Basic information

Entry
Database: PDB / ID: 9h8z
TitleFAD-dependent monooxygenase sorC with sorbicillin bound
ComponentsFAD-dependent monooxygenase sorC
KeywordsOXIDOREDUCTASE / Flavin / FAD / natural product / monooxygenase / sorbicillinoids
Function / homology
Function and homology information


Oxidoreductases / secondary metabolite biosynthetic process / FAD binding / monooxygenase activity / membrane
Similarity search - Function
: / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / FLAVIN-ADENINE DINUCLEOTIDE / FAD-dependent monooxygenase sorC
Similarity search - Component
Biological speciesPenicillium rubens Wisconsin 54-1255 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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

Downloads & links

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Assembly

Deposited unit
A: FAD-dependent monooxygenase sorC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2313
Polymers48,2131
Non-polymers1,0182
Water4,666259
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-6 kcal/mol
Surface area16630 Å2
Unit cell
Length a, b, c (Å)42.321, 90.965, 94.552
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FAD-dependent monooxygenase sorC / Sorbicillinoid biosynthetic cluster protein C


Mass: 48213.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium rubens Wisconsin 54-1255 (fungus)
Gene: sorC, Pc21g05060 / Production host: Escherichia coli (E. coli) / References: UniProt: B6HN76, Oxidoreductases
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-A1ITD / (2~{Z})-1-[3,5-dimethyl-2,4-bis(oxidanyl)phenyl]hexa-2,4-dien-1-one


Mass: 232.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.89 Å3/Da / Density % sol: 34.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.2 M ammonium citrate dibasic, 20% PEG3350, 1 mM sorbicillin, 1 mM NAD+

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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: Mar 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.71→42.32 Å / Num. obs: 38849 / % possible obs: 96.4 % / Redundancy: 4.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.028 / Rrim(I) all: 0.06 / Χ2: 0.99 / Net I/σ(I): 13.1 / Num. measured all: 165546
Reflection shellResolution: 1.71→1.74 Å / % possible obs: 86.8 % / Redundancy: 4.1 % / Rmerge(I) obs: 1.019 / Num. measured all: 7416 / Num. unique obs: 1814 / CC1/2: 0.528 / Rpim(I) all: 0.547 / Rrim(I) all: 1.163 / Χ2: 0.92 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→38.66 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.892 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22737 1916 4.9 %RANDOM
Rwork0.17237 ---
obs0.17494 36899 95.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.736 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0 Å2-0 Å2
2---0.11 Å20 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 1.71→38.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3215 0 67 259 3541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123362
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163106
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.8124586
X-RAY DIFFRACTIONr_angle_other_deg0.5611.7387107
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3445432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.1265.51729
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.24210497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0780.2519
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024072
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02783
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_it2.4212.771725
X-RAY DIFFRACTIONr_mcbond_other2.42.7691725
X-RAY DIFFRACTIONr_mcangle_it3.3714.9652155
X-RAY DIFFRACTIONr_mcangle_other3.3714.9662156
X-RAY DIFFRACTIONr_scbond_it3.2133.0611637
X-RAY DIFFRACTIONr_scbond_other3.1993.0611637
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7655.4912431
X-RAY DIFFRACTIONr_long_range_B_refined6.29729.153830
X-RAY DIFFRACTIONr_long_range_B_other6.30828.543788
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.71→1.751 Å
RfactorNum. reflection% reflection
Rfree0.394 137 -
Rwork0.363 2438 -
obs--87.5 %

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