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- PDB-8qd3: Ayg1p in complex with 1,3,6,8-Tetrahydroxynaphthalene -

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Basic information

Entry
Database: PDB / ID: 8qd3
TitleAyg1p in complex with 1,3,6,8-Tetrahydroxynaphthalene
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 / FLAVIOLIN / TRIETHYLENE GLYCOL / : / Heptaketide hydrolyase ayg1
Function and homology information
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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

Downloads & links

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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)192,60420
Polymers189,7624
Non-polymers2,84216
Water18,5011027
1
A: Pigment biosynthesis protein yellowish-green 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1955
Polymers47,4401
Non-polymers7554
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)48,1075
Polymers47,4401
Non-polymers6674
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)48,2576
Polymers47,4401
Non-polymers8175
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)48,0454
Polymers47,4401
Non-polymers6043
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.480, 107.440, 92.720
Angle α, β, γ (deg.)90.00, 90.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 1043 molecules

#2: Chemical
ChemComp-QW8 / naphthalene-1,3,6,8-tetrol / 1,3,6,8-tetrahydroxynaphthalene


Mass: 192.168 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H8O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-FLV / FLAVIOLIN / 2,5,7-TRIHYDROXYNAPHTHOQUINONE


Mass: 206.152 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H6O5
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1027 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 45.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM K/Na tartrate, 25.5% 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: Nov 27, 2021
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: 173708 / % possible obs: 94.6 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 6.7
Reflection shellResolution: 1.7→1.8 Å / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 27645 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→46.48 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.265 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22115 8775 5.1 %RANDOM
Rwork0.1963 ---
obs0.19754 164908 93.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.791 Å2
Baniso -1Baniso -2Baniso -3
1--22.38 Å2-0 Å210.63 Å2
2--37.13 Å20 Å2
3----14.74 Å2
Refinement stepCycle: 1 / Resolution: 1.7→46.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12386 0 204 1028 13618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01313091
X-RAY DIFFRACTIONr_bond_other_d0.0010.01511824
X-RAY DIFFRACTIONr_angle_refined_deg1.1941.64217927
X-RAY DIFFRACTIONr_angle_other_deg1.1321.57427239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.22251624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.13221.641658
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.529151919
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3021577
X-RAY DIFFRACTIONr_chiral_restr0.0490.21666
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215002
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023024
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_it1.0322.1696415
X-RAY DIFFRACTIONr_mcbond_other1.0322.1686414
X-RAY DIFFRACTIONr_mcangle_it1.3923.2578027
X-RAY DIFFRACTIONr_mcangle_other1.3923.2578028
X-RAY DIFFRACTIONr_scbond_it0.9282.2566676
X-RAY DIFFRACTIONr_scbond_other0.9272.2566677
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2133.3529888
X-RAY DIFFRACTIONr_long_range_B_refined2.26925.97415447
X-RAY DIFFRACTIONr_long_range_B_other2.26925.97415448
X-RAY DIFFRACTIONr_rigid_bond_restr0.474324913
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.739 Å
RfactorNum. reflection% reflection
Rfree0.264 611 -
Rwork0.198 11047 -
obs--85.87 %

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