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- PDB-8qd4: Ayg1p active site converted to tetrahedral sulfonate ester -

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Basic information

Entry
Database: PDB / ID: 8qd4
TitleAyg1p active site converted to tetrahedral sulfonate ester
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 / phenylmethanesulfonic acid / Heptaketide hydrolyase ayg1
Function and homology information
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
Revision 1.3Nov 13, 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
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)190,4508
Polymers189,7624
Non-polymers6894
Water7,819434
1
A: Pigment biosynthesis protein yellowish-green 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6132
Polymers47,4401
Non-polymers1721
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)47,6132
Polymers47,4401
Non-polymers1721
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)47,6132
Polymers47,4401
Non-polymers1721
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)47,6132
Polymers47,4401
Non-polymers1721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.640, 107.550, 92.540
Angle α, β, γ (deg.)90.00, 90.01, 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-PMS / phenylmethanesulfonic acid


Mass: 172.202 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C7H8O3S / Source: (gene. exp.) Aspergillus fumigatus (mold) / Plasmid: pRSET A / Production host: Escherichia coli BL21(DE3) (bacteria) / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / Source method: isolated from a natural source / Formula: H2O
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: 2.24 Å3/Da / Density % sol: 45.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 150 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: Jan 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 148659 / % possible obs: 95.9 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 9.4
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 22485 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→46.49 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.231 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24649 7356 4.9 %RANDOM
Rwork0.23529 ---
obs0.23586 141275 95.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.806 Å2
Baniso -1Baniso -2Baniso -3
1--14.57 Å2-0 Å24.68 Å2
2--37.59 Å20 Å2
3----23.03 Å2
Refinement stepCycle: 1 / Resolution: 1.8→46.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12344 0 10 434 12788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01312827
X-RAY DIFFRACTIONr_bond_other_d0.0010.01511627
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.64317570
X-RAY DIFFRACTIONr_angle_other_deg1.1281.57426747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.551614
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95521.768639
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.228151855
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5171575
X-RAY DIFFRACTIONr_chiral_restr0.0510.21665
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214693
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022981
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_it1.0582.9146405
X-RAY DIFFRACTIONr_mcbond_other1.0582.9146404
X-RAY DIFFRACTIONr_mcangle_it1.6514.3698012
X-RAY DIFFRACTIONr_mcangle_other1.6514.3698013
X-RAY DIFFRACTIONr_scbond_it0.8162.9236422
X-RAY DIFFRACTIONr_scbond_other0.8162.9236423
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2744.3759550
X-RAY DIFFRACTIONr_long_range_B_refined3.08534.18514621
X-RAY DIFFRACTIONr_long_range_B_other3.02334.16114579
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 538 -
Rwork0.338 10423 -
obs--96.36 %

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