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- PDB-8bxl: Patulin Synthase from Penicillium expansum -

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Basic information

Entry
Database: PDB / ID: 8bxl
TitlePatulin Synthase from Penicillium expansum
ComponentsPatulin synthase
KeywordsFLAVOPROTEIN / Oxidoreductase / GMC-type flavoprotein / Biocatalysis
Function / homology
Function and homology information


patulin biosynthetic process / Oxidoreductases; Acting on the CH-OH group of donors / polyketide synthase activity / oxidoreductase activity, acting on CH-OH group of donors / vacuole / extracellular matrix / flavin adenine dinucleotide binding / cell cortex / oxidoreductase activity / extracellular region
Similarity search - Function
GMC oxidoreductases signature 2. / Glucose-methanol-choline oxidoreductase / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Patulin synthase
Similarity search - Component
Biological speciesPenicillium expansum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTjallinks, G. / Boverio, A. / Rozeboom, H.J. / Fraaije, M.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Febs J. / Year: 2023
Title: Structure elucidation and characterization of patulin synthase, insights into the formation of a fungal mycotoxin.
Authors: Tjallinks, G. / Boverio, A. / Maric, I. / Rozeboom, H. / Arentshorst, M. / Visser, J. / Ram, A.F.J. / Mattevi, A. / Fraaije, M.W.
History
DepositionDec 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Patulin synthase
C: Patulin synthase
D: Patulin synthase
A: Patulin synthase
F: Patulin synthase
E: Patulin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)425,33669
Polymers409,1896
Non-polymers16,14663
Water17,637979
1
B: Patulin synthase
A: Patulin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,83723
Polymers136,3962
Non-polymers5,44121
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Patulin synthase
D: Patulin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,51920
Polymers136,3962
Non-polymers5,12318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: Patulin synthase
E: Patulin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,98026
Polymers136,3962
Non-polymers5,58324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.841, 144.163, 155.240
Angle α, β, γ (deg.)90.00, 91.53, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
99
1010
1111
1212
1313
1414
1515

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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Protein , 1 types, 6 molecules BCDAFE

#1: Protein
Patulin synthase / Dehydrogenase patE / Patulin biosynthesis cluster protein E


Mass: 68198.242 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium expansum (fungus) / Gene: patE, PEX2_082770 / Production host: Aspergillus niger (mold)
References: UniProt: A0A075TRK9, Oxidoreductases; Acting on the CH-OH group of donors

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Sugars , 3 types, 30 molecules

#2: Polysaccharide
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+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.: 1
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.: 24 / 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 , 4 types, 1012 molecules

#4: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 979 / 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: 2.87 Å3/Da / Density % sol: 57.08 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: Calcium chloride, PEG6000 and sodium acetate pH 5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 2.4→48.74 Å / Num. obs: 179872 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.978 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.064 / Rrim(I) all: 0.168 / Χ2: 0.81 / Net I/σ(I): 9.5
Reflection shellResolution: 2.4→2.44 Å / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 1.113 / Num. measured all: 60753 / Num. unique obs: 8892 / CC1/2: 0.72 / Rpim(I) all: 0.47 / Rrim(I) all: 1.211 / Χ2: 0.48 / Net I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMACv7.1.018refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→48.74 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.163 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.326 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22244 9411 5.2 %RANDOM
Rwork0.18222 ---
obs0.18429 170431 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: 37.378 Å2
Baniso -1Baniso -2Baniso -3
1-2.32 Å2-0 Å2-1.6 Å2
2---0.22 Å2-0 Å2
3----2.02 Å2
Refinement stepCycle: 1 / Resolution: 2.4→48.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27028 0 1059 979 29066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01328837
X-RAY DIFFRACTIONr_bond_other_d0.0010.01526069
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.67439388
X-RAY DIFFRACTIONr_angle_other_deg1.2631.59859957
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.37953534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.42322.0451438
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.676154047
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.58115175
X-RAY DIFFRACTIONr_chiral_restr0.0660.23871
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0233047
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026779
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_it5.9297.33814154
X-RAY DIFFRACTIONr_mcbond_other5.9287.33814153
X-RAY DIFFRACTIONr_mcangle_it7.16813.77717682
X-RAY DIFFRACTIONr_mcangle_other7.16813.77817683
X-RAY DIFFRACTIONr_scbond_it8.0928.49614683
X-RAY DIFFRACTIONr_scbond_other8.0928.49614684
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.17915.36221707
X-RAY DIFFRACTIONr_long_range_B_refined10.66148.61631273
X-RAY DIFFRACTIONr_long_range_B_other10.66148.61631274
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B194280.04
12C194280.04
21B192060.04
22D192060.04
31B194510.05
32A194510.05
41B194470.04
42F194470.04
51B193830.05
52E193830.05
61C192050.04
62D192050.04
71C193170.05
72A193170.05
81C193530.04
82F193530.04
91C193080.05
92E193080.05
101D192020.04
102A192020.04
111D192000.04
112F192000.04
121D191410.04
122E191410.04
131A194490.05
132F194490.05
141A195700.03
142E195700.03
151F194550.04
152E194550.04
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 677 -
Rwork0.229 12580 -
obs--99.99 %

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