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- PDB-9qde: Crystal structure of the non-glycosylated polyester hydrolase Lei... -

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Basic information

Entry
Database: PDB / ID: 9qde
TitleCrystal structure of the non-glycosylated polyester hydrolase Leipzig 7 (PHL7) mut3 variant expressed in Pichia pastoris (P_PHL7mut3_ng)
ComponentsPolyester Hydrolase Leipzig 7 (PHL-7), catalysis-deficient S131A mutant
KeywordsHYDROLASE / E. coli / LCC / K. phaffii / PETase / P. pastoris
Function / homologyCutinase / PET hydrolase-like / : / hydrolase activity, acting on ester bonds / Alpha/Beta hydrolase fold / Polyester Hydrolase Leipzig 7 (PHL-7), catalysis-deficient S131A mutant
Function and homology information
Biological speciescompost metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 Å
AuthorsUseini, A. / Strater, N. / Striedner, G. / Sonnendecker, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)European Union's Horizon 2020 research and inovation, 887913 (Enzycle)European Union
CitationJournal: ACS ES T Eng / Year: 2025
Title: Trade-Offs between Stability and Activity of Glycosylated and Non-Glycosylated Polyester Hydrolases PHL7 and PHL7mut3
Authors: Fohler, L. / Faschingeder, F. / Leibetseder, L. / Zhao, Z. / Useini, A. / Strater, N. / Sonnendecker, C. / Ewing, T.A. / Moers, A.P.H.A. / Werten, M.W.T. / van Vliet, D.M. / Julsing, M.K. / ...Authors: Fohler, L. / Faschingeder, F. / Leibetseder, L. / Zhao, Z. / Useini, A. / Strater, N. / Sonnendecker, C. / Ewing, T.A. / Moers, A.P.H.A. / Werten, M.W.T. / van Vliet, D.M. / Julsing, M.K. / Zimmermann, W. / Striedner, G.
History
DepositionMar 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyester Hydrolase Leipzig 7 (PHL-7), catalysis-deficient S131A mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7632
Polymers28,7281
Non-polymers351
Water7,981443
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-11 kcal/mol
Surface area10090 Å2
Unit cell
Length a, b, c (Å)46.052, 59.014, 86.151
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Polyester Hydrolase Leipzig 7 (PHL-7), catalysis-deficient S131A mutant


Mass: 28727.900 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) compost metagenome (others) / Production host: Pichia (fungus) / References: UniProt: A0AA82WPD4
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.04 Å3/Da / Density % sol: 39.63 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bicine (pH 9.0), 5% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.02→48.69 Å / Num. obs: 90273 / % possible obs: 93.7 % / Redundancy: 7.9 % / Biso Wilson estimate: 11.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.016 / Rrim(I) all: 0.058 / Net I/σ(I): 18.4
Reflection shellResolution: 1.02→1.12 Å / Rmerge(I) obs: 1.147 / Num. unique obs: 4515 / CC1/2: 0.566 / Rpim(I) all: 0.42

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
STARANISOdata scaling
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.02→27.92 Å / SU ML: 0.0768 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.0519
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1496 1776 1.97 %
Rwork0.1238 88482 -
obs0.1243 90258 76.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.99 Å2
Refinement stepCycle: LAST / Resolution: 1.02→27.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1994 0 1 443 2438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112168
X-RAY DIFFRACTIONf_angle_d1.12492976
X-RAY DIFFRACTIONf_chiral_restr0.0863325
X-RAY DIFFRACTIONf_plane_restr0.0145402
X-RAY DIFFRACTIONf_dihedral_angle_d13.5695800
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.02-1.050.423640.2873291X-RAY DIFFRACTION3.28
1.05-1.080.2374260.26821367X-RAY DIFFRACTION15.56
1.08-1.120.2338650.2362916X-RAY DIFFRACTION32.98
1.12-1.160.20861110.20745448X-RAY DIFFRACTION62.04
1.16-1.20.23561580.18377560X-RAY DIFFRACTION85.34
1.2-1.260.17911660.16498295X-RAY DIFFRACTION94.16
1.26-1.330.18761780.148697X-RAY DIFFRACTION97.88
1.33-1.410.19271840.12288823X-RAY DIFFRACTION99.42
1.41-1.520.13891760.10678867X-RAY DIFFRACTION99.71
1.52-1.670.1251700.09678921X-RAY DIFFRACTION99.84
1.67-1.910.12251650.10098975X-RAY DIFFRACTION99.84
1.91-2.410.11371850.11249031X-RAY DIFFRACTION100
2.41-27.920.15751880.12579291X-RAY DIFFRACTION99.42

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