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- PDB-8qd1: Ayg1p from A. fumigatus catalyzes polyketide shortening in the bi... -

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Basic information

Entry
Database: PDB / ID: 8qd1
TitleAyg1p from A. fumigatus catalyzes polyketide shortening in the biosynthesis of DHN-melanin
ComponentsPigment biosynthesis protein yellowish-green 1
KeywordsLYASE / Natural Product Biosynthesis / Polyketide Synthase System / alpha / beta-Hydrolase Fold / Polyketide Shortening / Retro Claisen Reaction
Function / homologyEsterase FrsA-like / Esterase FrsA-like / : / Alpha/Beta hydrolase fold / Heptaketide hydrolyase ayg1
Function and homology information
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsSchmalhofer, M. / Vagstad, A.L. / Zhou, Q. / Bode, H.B. / Groll, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB 1309 - 325871075 Germany
CitationJournal: Adv Sci / Year: 2024
Title: Polyketide Trimming Shapes Dihydroxynaphthalene-Melanin and Anthraquinone Pigments.
Authors: Schmalhofer, M. / Vagstad, A.L. / Zhou, Q. / Bode, H.B. / Groll, M.
History
DepositionAug 28, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 19, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pigment biosynthesis protein yellowish-green 1
B: Pigment biosynthesis protein yellowish-green 1
C: Pigment biosynthesis protein yellowish-green 1
D: Pigment biosynthesis protein yellowish-green 1


Theoretical massNumber of molelcules
Total (without water)189,7624
Polymers189,7624
Non-polymers00
Water31,4001743
1
A: Pigment biosynthesis protein yellowish-green 1


Theoretical massNumber of molelcules
Total (without water)47,4401
Polymers47,4401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pigment biosynthesis protein yellowish-green 1


Theoretical massNumber of molelcules
Total (without water)47,4401
Polymers47,4401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Pigment biosynthesis protein yellowish-green 1


Theoretical massNumber of molelcules
Total (without water)47,4401
Polymers47,4401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Pigment biosynthesis protein yellowish-green 1


Theoretical massNumber of molelcules
Total (without water)47,4401
Polymers47,4401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.830, 108.480, 91.890
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pigment biosynthesis protein yellowish-green 1


Mass: 47440.410 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: ayg1 / Plasmid: pRSET A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UVV1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1743 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100-200 mM K/Na tartrate, 15-26% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 179315 / % possible obs: 97.2 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 9.6
Reflection shellResolution: 1.7→1.8 Å / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 28397 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→46.71 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.61 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19864 8937 5 %RANDOM
Rwork0.1659 ---
obs0.16757 170348 97.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.76 Å2
Baniso -1Baniso -2Baniso -3
1--12.1 Å2-0 Å20.91 Å2
2--32.1 Å20 Å2
3----20 Å2
Refinement stepCycle: 1 / Resolution: 1.7→46.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12383 0 0 1743 14126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01312880
X-RAY DIFFRACTIONr_bond_other_d0.0010.01511768
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.64217621
X-RAY DIFFRACTIONr_angle_other_deg1.1831.57427116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.27251620
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87321.772649
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.201151925
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8851577
X-RAY DIFFRACTIONr_chiral_restr0.0540.21664
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214738
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022988
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_it0.9121.7626414
X-RAY DIFFRACTIONr_mcbond_other0.9121.7616413
X-RAY DIFFRACTIONr_mcangle_it1.2422.6468026
X-RAY DIFFRACTIONr_mcangle_other1.2412.6468027
X-RAY DIFFRACTIONr_scbond_it0.841.8746466
X-RAY DIFFRACTIONr_scbond_other0.841.8746467
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1092.7719585
X-RAY DIFFRACTIONr_long_range_B_refined2.1922.51415387
X-RAY DIFFRACTIONr_long_range_B_other1.94321.67514913
X-RAY DIFFRACTIONr_rigid_bond_restr0.466324648
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.743 Å
RfactorNum. reflection% reflection
Rfree0.272 645 -
Rwork0.191 12404 -
obs--95.91 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7133-0.07410.21690.3399-0.0591.12780.0196-0.07770.03060.0245-0.0441-0.01380.0126-0.02750.02440.0325-0.0103-0.01310.01710.00060.038.55523.9761.709
20.7580.06160.11110.23470.05061.043-0.00110.06530.0402-0.0118-0.0101-0.0115-0.0061-0.01640.01110.03530.0031-0.00810.00740.00280.0314-15.32423.826-37.665
30.68110.0237-0.13550.2074-0.13221.33690.00630.0732-0.034-0.0298-0.0261-0.0056-0.01080.04270.01990.03780.00810.00660.0393-0.00330.0398-34.17626.9238.375
40.7427-0.0298-0.08770.30820.03610.99720.0274-0.0393-0.0270.0255-0.0406-0.00390.00510.0090.01320.0299-0.00580.00030.0080.00410.031627.81426.964-44.248
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 399
2X-RAY DIFFRACTION2B3 - 399
3X-RAY DIFFRACTION3C3 - 399
4X-RAY DIFFRACTION4D3 - 399

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