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- PDB-9qyb: Polyester Hydrolase Leipzig 7 (PHL7) variant R4M10 -

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Basic information

Entry
Database: PDB / ID: 9qyb
TitlePolyester Hydrolase Leipzig 7 (PHL7) variant R4M10
ComponentsPolyester Hydrolase Leipzig 7 (PHL7) variant R4M10
KeywordsHYDROLASE / PET hydrolase / enzymatic plastic degradation / enzyme engineering / Polyester Hydrolase Leipzig 7
Biological speciescompost metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.1 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 R4M10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5873
Polymers28,5161
Non-polymers712
Water5,296294
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-19 kcal/mol
Surface area9690 Å2
Unit cell
Length a, b, c (Å)80.717, 80.717, 138.042
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-302-

CL

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Components

#1: Protein Polyester Hydrolase Leipzig 7 (PHL7) variant R4M10


Mass: 28515.607 Da / Num. of mol.: 1
Mutation: E6Q, Q34D, D36S, E68S, T91S, L93F, Q95Y, 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.: 294 / 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: 2.28 Å3/Da / Density % sol: 45.96 %
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: P13 (MX1) / Wavelength: 0.7293 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7293 Å / Relative weight: 1
ReflectionResolution: 1.1→69.9 Å / Num. obs: 107770 / % possible obs: 100 % / Redundancy: 40 % / Biso Wilson estimate: 11.89 Å2 / CC1/2: 0.995 / Net I/σ(I): 9.6
Reflection shellResolution: 1.1→1.12 Å / Num. unique obs: 5279 / CC1/2: 0.581

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
REFMAC8refinement
XDSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.1→38.74 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1701 2162 2.01 %
Rwork0.1528 --
obs0.1531 107657 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.1→38.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1950 0 2 301 2253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013
X-RAY DIFFRACTIONf_angle_d1.187
X-RAY DIFFRACTIONf_dihedral_angle_d12.306778
X-RAY DIFFRACTIONf_chiral_restr0.096319
X-RAY DIFFRACTIONf_plane_restr0.016392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.130.25531350.26066929X-RAY DIFFRACTION100
1.13-1.150.24491260.23866955X-RAY DIFFRACTION100
1.15-1.180.24271450.21916923X-RAY DIFFRACTION100
1.18-1.220.20881650.20796920X-RAY DIFFRACTION100
1.22-1.260.22131470.19826946X-RAY DIFFRACTION100
1.26-1.30.18981380.17686946X-RAY DIFFRACTION100
1.3-1.360.18331540.17046929X-RAY DIFFRACTION100
1.36-1.420.1881540.16366974X-RAY DIFFRACTION100
1.42-1.490.16351440.14716999X-RAY DIFFRACTION100
1.49-1.590.1451520.13427006X-RAY DIFFRACTION100
1.59-1.710.14411270.13467040X-RAY DIFFRACTION100
1.71-1.880.16141570.13547056X-RAY DIFFRACTION100
1.88-2.150.15991320.13037114X-RAY DIFFRACTION100
2.15-2.710.13421420.13857196X-RAY DIFFRACTION100
2.71-38.740.17581440.14917562X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -5.4234 Å / Origin y: 26.7721 Å / Origin z: -5.1447 Å
111213212223313233
T0.091 Å2-0.011 Å20.0269 Å2-0.0647 Å2-0.0101 Å2--0.0721 Å2
L0.7144 °20.1049 °20.1265 °2-0.7153 °2-0.1307 °2--1.2366 °2
S0.0458 Å °-0.0081 Å °0.0559 Å °0.0714 Å °0.0075 Å °-0.0039 Å °-0.1329 Å °0.0618 Å °-0.0365 Å °
Refinement TLS groupSelection details: all

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