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- PDB-9qya: Polyester Hydrolase Leipzig 7 (PHL7) variant R4M6 -

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Basic information

Entry
Database: PDB / ID: 9qya
TitlePolyester Hydrolase Leipzig 7 (PHL7) variant R4M6
ComponentsPolyester Hydrolase Leipzig 7 (PHL7) variant R4M6
KeywordsHYDROLASE / PET hydrolase / enzymatic plastic degradation / enzyme engineering / Polyester Hydrolase Leipzig 7
Biological speciescompost metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsUseini, A. / Strater, N. / Kuenze, G. / Sonnendecker, C.
Funding supportEuropean Union, 2items
OrganizationGrant numberCountry
European Union (EU)State of Saxony, European Union's Just Transition Fund, grant nr 100704504European Union
European Union (EU)Horizon 2020 research and innovation program, grant nr 887913 (ENZYCLE)European Union
CitationJournal: Nat Commun / Year: 2026
Title: Computational engineering of the polyester hydrolase PHL7 for efficient poly(ethylene terephthalate) degradation in biocatalytic recycling processes.
Authors: Blazquez-Sanchez, P. / Gunkel, J. / Useini, A. / Zlobin, A. / Zakary, J.D. / Scholer, A. / Graefe, N. / Engelberger, F. / Cantanhede, F. / Frank, R. / Zhao, Z. / Zarei, A. / Butenschon, E. / ...Authors: Blazquez-Sanchez, P. / Gunkel, J. / Useini, A. / Zlobin, A. / Zakary, J.D. / Scholer, A. / Graefe, N. / Engelberger, F. / Cantanhede, F. / Frank, R. / Zhao, Z. / Zarei, A. / Butenschon, E. / Matysik, J. / Zimmermann, W. / Strater, N. / Sonnendecker, C. / Kunze, G.
History
DepositionApr 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2026Provider: 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 (PHL7) variant R4M6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8203
Polymers27,7491
Non-polymers712
Water4,918273
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-20 kcal/mol
Surface area9610 Å2
Unit cell
Length a, b, c (Å)80.375, 80.375, 137.818
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-302-

CL

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Components

#1: Protein Polyester Hydrolase Leipzig 7 (PHL7) variant R4M6


Mass: 27748.867 Da / Num. of mol.: 1
Mutation: E6Q, Q34D, D36S, E68S, T91S, H109Y, R111T, N113D, V115T, N118D, T145P, E148K, N161D, T167V, V171I, Q175E, D196S, D198P, L210T, D215N, L235T, F248P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) compost metagenome (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.32 Å3/Da / Density % sol: 46.88 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 1.1 M sodium malonate, 0.1 M HEPES pH 7.0, 0.5% (v/v) Jeffamine ED-2003

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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: P14 (MX2) / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.53→62.13 Å / Num. obs: 27315 / % possible obs: 96 % / Redundancy: 38.4 % / CC1/2: 0.9 / Net I/σ(I): 15.4
Reflection shellResolution: 1.53→1.71 Å / Num. unique obs: 1366 / CC1/2: 0.557

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Processing

Software
NameVersionClassification
PHENIX(1.20.1)refinement
REFMAC8refinement
PDB_EXTRACTdata extraction
XDSdata reduction
STARANISOdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→62.13 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1945 1876 6.87 %
Rwork0.157 --
obs0.1595 27313 67.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.53→62.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1944 0 2 274 2220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.726
X-RAY DIFFRACTIONf_dihedral_angle_d12.103743
X-RAY DIFFRACTIONf_chiral_restr0.047313
X-RAY DIFFRACTIONf_plane_restr0.01373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.570.313510.240954X-RAY DIFFRACTION2
1.57-1.620.3475110.2722235X-RAY DIFFRACTION8
1.62-1.670.2486460.2437496X-RAY DIFFRACTION18
1.67-1.730.2824550.2483790X-RAY DIFFRACTION28
1.73-1.80.2791010.23261146X-RAY DIFFRACTION41
1.8-1.880.24661660.20742186X-RAY DIFFRACTION76
1.88-1.980.22092080.19392822X-RAY DIFFRACTION99
1.98-2.110.20592150.16362870X-RAY DIFFRACTION100
2.11-2.270.16712110.14282865X-RAY DIFFRACTION100
2.27-2.50.19562220.13292898X-RAY DIFFRACTION100
2.5-2.860.18151980.14942940X-RAY DIFFRACTION100
2.86-3.60.18032060.14712977X-RAY DIFFRACTION100
3.6-62.130.19272360.15543158X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -5.4514 Å / Origin y: 26.8088 Å / Origin z: -4.7353 Å
111213212223313233
T0.1224 Å2-0.0051 Å20.0183 Å2-0.1055 Å2-0.0098 Å2--0.1144 Å2
L0.5044 °20.1234 °20.0641 °2-0.5518 °2-0.1018 °2--0.9497 °2
S0.0313 Å °-0.005 Å °0.0366 Å °0.0571 Å °-0.001 Å °-0.0061 Å °-0.1235 Å °0.0299 Å °0.0002 Å °
Refinement TLS groupSelection details: all

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