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- PDB-8qd8: Wdyg1p in complex with 1,3-Dihydroxynaphthalene -

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Basic information

Entry
Database: PDB / ID: 8qd8
TitleWdyg1p in complex with 1,3-Dihydroxynaphthalene
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: 1.65 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: Yellowish-green 1-like protein
B: Yellowish-green 1-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9046
Polymers98,4602
Non-polymers4444
Water13,637757
1
A: Yellowish-green 1-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5144
Polymers49,2301
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Yellowish-green 1-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3902
Polymers49,2301
Non-polymers1601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.800, 88.850, 123.050
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-QPI / naphthalene-1,3-diol / 1,3-Dihydroxynaphthalene


Mass: 160.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H8O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 757 / 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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7 / Details: 100 mM tris pH 8.7, 24% 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 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 111963 / % possible obs: 98.7 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 11.8
Reflection shellResolution: 1.65→1.75 Å / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 17823 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→43.57 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.778 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.018 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18807 5598 5 %RANDOM
Rwork0.16346 ---
obs0.16469 106353 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.512 Å2
Baniso -1Baniso -2Baniso -3
1-1.99 Å2-0 Å2-0 Å2
2--9.47 Å20 Å2
3----11.47 Å2
Refinement stepCycle: 1 / Resolution: 1.65→43.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6604 0 32 757 7393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0136871
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166419
X-RAY DIFFRACTIONr_angle_refined_deg1.161.6459303
X-RAY DIFFRACTIONr_angle_other_deg1.1741.5814904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0965833
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.24222.798336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.841151198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.61532
X-RAY DIFFRACTIONr_chiral_restr0.0550.2854
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027657
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021519
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_it0.7061.83323
X-RAY DIFFRACTIONr_mcbond_other0.7041.83322
X-RAY DIFFRACTIONr_mcangle_it0.9152.7064159
X-RAY DIFFRACTIONr_mcangle_other0.9152.7064160
X-RAY DIFFRACTIONr_scbond_it0.7621.9683548
X-RAY DIFFRACTIONr_scbond_other0.7621.9693549
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9712.8925145
X-RAY DIFFRACTIONr_long_range_B_refined1.71522.8238206
X-RAY DIFFRACTIONr_long_range_B_other1.71522.8238207
X-RAY DIFFRACTIONr_rigid_bond_restr0.482313290
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 405 -
Rwork0.253 7695 -
obs--98.25 %
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)
10.8465-0.07780.24410.7210.15111.0928-0.00090.1057-0.0568-0.0614-0.06050.07630.01860.01390.06140.07490.0140.00320.0182-0.01170.10032.44517.61221.88
21.10430.08070.14120.50890.00930.6864-0.02080.09720.1245-0.0437-0.0184-0.1012-0.04570.16260.03920.0501-0.00160.00480.11270.05310.134442.70123.27544.261
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 411
2X-RAY DIFFRACTION2B1 - 412

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