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- PDB-8qd9: Wdyg1p in complex with 1,3,6,8-Tetrahydroxynaphthalene -

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Basic information

Entry
Database: PDB / ID: 8qd9
TitleWdyg1p in complex with 1,3,6,8-Tetrahydroxynaphthalene
ComponentsYellowish-green 1-like protein
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 / : / Yellowish-green 1-like protein
Function and homology information
Biological speciesExophiala dermatitidis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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: Yellowish-green 1-like protein
B: Yellowish-green 1-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9686
Polymers98,4602
Non-polymers5084
Water9,206511
1
A: Yellowish-green 1-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4222
Polymers49,2301
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Yellowish-green 1-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5464
Polymers49,2301
Non-polymers3163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.220, 88.490, 122.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Yellowish-green 1-like protein


Mass: 49230.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Exophiala dermatitidis (fungus) / Gene: yg1 / Plasmid: pCDFDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6BCB5
#2: Chemical ChemComp-QW8 / naphthalene-1,3,6,8-tetrol / 1,3,6,8-tetrahydroxynaphthalene


Mass: 192.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H8O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 511 / 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: 2.37 Å3/Da / Density % sol: 48.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM tris pH 8.5, 21% 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: Feb 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 67832 / % possible obs: 98.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 14.1
Reflection shellResolution: 1.95→2.05 Å / Rmerge(I) obs: 0.638 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 9135 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→43.46 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 5.799 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20337 3391 5 %RANDOM
Rwork0.15804 ---
obs0.1603 64426 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.131 Å2
Baniso -1Baniso -2Baniso -3
1-21.62 Å20 Å20 Å2
2---22.08 Å2-0 Å2
3---0.45 Å2
Refinement stepCycle: 1 / Resolution: 1.95→43.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6521 0 36 511 7068
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0136743
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166240
X-RAY DIFFRACTIONr_angle_refined_deg1.2041.6449144
X-RAY DIFFRACTIONr_angle_other_deg1.1811.57914448
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3515822
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.43722.71321
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.205151129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7411530
X-RAY DIFFRACTIONr_chiral_restr0.0570.2848
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027528
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021492
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_it1.2972.4643294
X-RAY DIFFRACTIONr_mcbond_other1.2962.4633293
X-RAY DIFFRACTIONr_mcangle_it1.7143.6954114
X-RAY DIFFRACTIONr_mcangle_other1.7143.6964115
X-RAY DIFFRACTIONr_scbond_it1.3082.623449
X-RAY DIFFRACTIONr_scbond_other1.3082.623450
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7133.8735031
X-RAY DIFFRACTIONr_long_range_B_refined2.58829.9698009
X-RAY DIFFRACTIONr_long_range_B_other2.46629.5247897
X-RAY DIFFRACTIONr_rigid_bond_restr0.679312983
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 245 -
Rwork0.219 4648 -
obs--97.2 %
Refinement TLS params.

S12: 0.1031 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (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)
10.8598-0.19790.30441.05120.121.1796-0.0135-0.0913-0.0378-0.08430.1168-0.0237-0.01470.09790.03080.01840.00960.069-0.01660.03732.58317.71521.6
21.25690.07350.22960.8840.04661.1624-0.03810.1698-0.0953-0.0538-0.194-0.09270.26730.09190.0172-0.01290.01320.20780.09660.101442.54322.93643.948
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 411
2X-RAY DIFFRACTION2B1 - 413

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