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- PDB-8qd2: Ayg1p in complex with 1,3-Dihydroxynaphthalene -

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Basic information

Entry
Database: PDB / ID: 8qd2
TitleAyg1p in complex with 1,3-Dihydroxynaphthalene
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 / MOLECULAR REPLACEMENT / Resolution: 1.75 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,4028
Polymers189,7624
Non-polymers6414
Water21,5641197
1
A: Pigment biosynthesis protein yellowish-green 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6012
Polymers47,4401
Non-polymers1601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pigment biosynthesis protein yellowish-green 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6012
Polymers47,4401
Non-polymers1601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Pigment biosynthesis protein yellowish-green 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6012
Polymers47,4401
Non-polymers1601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Pigment biosynthesis protein yellowish-green 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6012
Polymers47,4401
Non-polymers1601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.470, 107.480, 92.510
Angle α, β, γ (deg.)90.00, 90.14, 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: Chemical
ChemComp-QPI / naphthalene-1,3-diol / 1,3-Dihydroxynaphthalene


Mass: 160.169 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H8O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1197 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM K/Na tartrate, 25% 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: Aug 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 159406 / % possible obs: 94.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 6.5
Reflection shellResolution: 1.75→1.85 Å / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 24753 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→46.47 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.47 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23865 7932 5 %RANDOM
Rwork0.2286 ---
obs0.22909 151446 94.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.861 Å2
Baniso -1Baniso -2Baniso -3
1--2.8 Å2-0 Å2-1.34 Å2
2--19.64 Å20 Å2
3----16.85 Å2
Refinement stepCycle: 1 / Resolution: 1.75→46.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12406 0 48 1198 13652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01312916
X-RAY DIFFRACTIONr_bond_other_d0.0010.01511769
X-RAY DIFFRACTIONr_angle_refined_deg1.2111.64117664
X-RAY DIFFRACTIONr_angle_other_deg1.1711.57427102
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.38251608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99121.792653
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.763151918
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2981577
X-RAY DIFFRACTIONr_chiral_restr0.0510.21658
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214748
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023006
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_it0.6492.1916396
X-RAY DIFFRACTIONr_mcbond_other0.6482.196395
X-RAY DIFFRACTIONr_mcangle_it1.0813.2847998
X-RAY DIFFRACTIONr_mcangle_other1.0813.2857999
X-RAY DIFFRACTIONr_scbond_it0.6342.2486520
X-RAY DIFFRACTIONr_scbond_other0.6342.2486521
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0383.359661
X-RAY DIFFRACTIONr_long_range_B_refined2.75926.37915266
X-RAY DIFFRACTIONr_long_range_B_other2.52726.06114987
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.792 Å
RfactorNum. reflection% reflection
Rfree0.301 540 -
Rwork0.28 10437 -
obs--88.6 %

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