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- PDB-9qbn: Crystal structure of the polyester hydrolase Leipzig 7 (PHL7) mut... -

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Basic information

Entry
Database: PDB / ID: 9qbn
TitleCrystal structure of the polyester hydrolase Leipzig 7 (PHL7) mut3 variant with glycosylation by expression in Pichia pastoris (P_PHL7mut3)
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 / metal ion binding / 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: 1.37 Å
AuthorsUseini, A. / Strater, N. / Striedner, G. / Sonnendecker, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)887913European 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 3, 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)29,4344
Polymers28,8171
Non-polymers6173
Water8,017445
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-10 kcal/mol
Surface area10890 Å2
Unit cell
Length a, b, c (Å)45.422, 63.997, 101.025
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: 28817.010 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: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Lithium Sulfate, 0.1 M Tris-HCl (pH 8.5), 30% w/v PEG 4000

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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 PILATUS 6M / 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: 1.37→101.03 Å / Num. obs: 47787 / % possible obs: 89.8 % / Redundancy: 8 % / Biso Wilson estimate: 11.76 Å2 / CC1/2: 0.995 / Net I/σ(I): 7.7
Reflection shellResolution: 1.37→1.49 Å / Num. unique obs: 2389 / CC1/2: 0.375

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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: 1.37→41.43 Å / SU ML: 0.1336 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.6219
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1684 2135 4.04 %
Rwork0.1335 50707 -
obs0.1349 47787 84.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.73 Å2
Refinement stepCycle: LAST / Resolution: 1.37→41.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2021 0 38 445 2504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00342176
X-RAY DIFFRACTIONf_angle_d0.72522982
X-RAY DIFFRACTIONf_chiral_restr0.0672332
X-RAY DIFFRACTIONf_plane_restr0.0081395
X-RAY DIFFRACTIONf_dihedral_angle_d12.1376818
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.40.3207560.29331459X-RAY DIFFRACTION36.75
1.4-1.440.3121830.27181716X-RAY DIFFRACTION43.91
1.44-1.480.32121040.25392144X-RAY DIFFRACTION54.29
1.48-1.520.2757920.22092755X-RAY DIFFRACTION69.05
1.52-1.570.24291350.19773586X-RAY DIFFRACTION90.01
1.57-1.620.23461530.17973816X-RAY DIFFRACTION96.17
1.62-1.690.17671590.16883852X-RAY DIFFRACTION96.74
1.69-1.770.20731670.16253852X-RAY DIFFRACTION96.96
1.77-1.860.21391660.14573868X-RAY DIFFRACTION97.18
1.86-1.980.1821680.1263743X-RAY DIFFRACTION93.63
1.98-2.130.1471800.11043942X-RAY DIFFRACTION98.71
2.13-2.340.13851680.10343937X-RAY DIFFRACTION98.23
2.34-2.680.13151470.1033952X-RAY DIFFRACTION96.67
2.68-3.380.14451630.10853996X-RAY DIFFRACTION97.84
3.38-41.430.14521940.12634089X-RAY DIFFRACTION96.18

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