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- PDB-9h8m: FAD-dependent monooxygenase sorC -

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Basic information

Entry
Database: PDB / ID: 9h8m
TitleFAD-dependent monooxygenase sorC
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 / DI(HYDROXYETHYL)ETHER / FAD-dependent monooxygenase sorC
Similarity search - Component
Biological speciesPenicillium rubens (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 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-dependent monooxygenase sorC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2114
Polymers48,2131
Non-polymers9983
Water7,674426
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-1 kcal/mol
Surface area17270 Å2
Unit cell
Length a, b, c (Å)45.817, 92.831, 98.164
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 (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 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.16 Å3/Da / Density % sol: 43.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5 / Details: 0.2 M MgCl2, 0.1 M Tri pH 8.5, 20% W/V PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.38→67.45 Å / Num. obs: 85417 / % possible obs: 98.8 % / Redundancy: 4.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.024 / Rrim(I) all: 0.053 / Χ2: 1.06 / Net I/σ(I): 13.4 / Num. measured all: 379985
Reflection shellResolution: 1.38→1.4 Å / % possible obs: 97 % / Redundancy: 3.6 % / Rmerge(I) obs: 1.124 / Num. measured all: 14715 / Num. unique obs: 4104 / CC1/2: 0.543 / Rpim(I) all: 0.663 / Rrim(I) all: 1.312 / Χ2: 0.99 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.38→43.43 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.298 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20217 4410 5.2 %RANDOM
Rwork0.17802 ---
obs0.17932 80926 98.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.931 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å2-0 Å20 Å2
2---0.02 Å2-0 Å2
3----1.32 Å2
Refinement stepCycle: 1 / Resolution: 1.38→43.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3256 0 67 426 3749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123410
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163179
X-RAY DIFFRACTIONr_angle_refined_deg1.8891.8164637
X-RAY DIFFRACTIONr_angle_other_deg0.6431.7457301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2235433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.653528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.05110529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0940.2519
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024108
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02791
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_it2.1182.1271726
X-RAY DIFFRACTIONr_mcbond_other2.0932.1271726
X-RAY DIFFRACTIONr_mcangle_it2.8923.8192158
X-RAY DIFFRACTIONr_mcangle_other2.8943.822159
X-RAY DIFFRACTIONr_scbond_it3.1022.4251684
X-RAY DIFFRACTIONr_scbond_other3.1022.4281685
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6374.2972479
X-RAY DIFFRACTIONr_long_range_B_refined5.47622.293929
X-RAY DIFFRACTIONr_long_range_B_other5.405213812
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.38→1.416 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 315 -
Rwork0.318 5824 -
obs--97.01 %

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