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- PDB-9qyc: Polyester Hydrolase Leipzig 7 (PHL7) variant R4M12 -

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Basic information

Entry
Database: PDB / ID: 9qyc
TitlePolyester Hydrolase Leipzig 7 (PHL7) variant R4M12
ComponentsPolyester Hydrolase Leipzig 7 (PHL7) variant R4M12
KeywordsHYDROLASE / PET hydrolase / enzymatic plastic degradation / enzyme engineering / Polyester Hydrolase Leipzig 7
Function / homologyCITRIC ACID
Function and homology information
Biological speciescompost metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.16 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 R4M12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4392
Polymers28,2461
Non-polymers1921
Water7,008389
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint4 kcal/mol
Surface area9980 Å2
Unit cell
Length a, b, c (Å)74.772, 74.772, 106.823
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Polyester Hydrolase Leipzig 7 (PHL7) variant R4M12


Mass: 28246.393 Da / Num. of mol.: 1
Mutation: E6Q, Q34D, D36S, E68S, T91S, L93F, Q95Y, H109Y, R111T, N113D, V115T, N118D, T145P, N161D, T167V, V171I, Q175E, D196S, D198P, L210T, D215N, D233K, L235T, F248
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) compost metagenome (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 2.64 Å3/Da / Density % sol: 53.46 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate pH 5.6, 20% PEG 4000, 20% (v/v) isopropanol

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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: 0.97625 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: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.16→52.87 Å / Num. obs: 93166 / % possible obs: 94 % / Redundancy: 26.6 % / CC1/2: 0.997 / Net I/σ(I): 13.1
Reflection shellResolution: 1.16→1.22 Å / Num. unique obs: 4659 / CC1/2: 0.363

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419)refinement
PDB_EXTRACTdata extraction
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.16→32.15 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1483 1925 2.07 %
Rwork0.1208 --
obs0.1214 93155 89.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.16→32.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1981 0 13 392 2386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014
X-RAY DIFFRACTIONf_angle_d1.469
X-RAY DIFFRACTIONf_dihedral_angle_d12.093814
X-RAY DIFFRACTIONf_chiral_restr0.103326
X-RAY DIFFRACTIONf_plane_restr0.021412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.16-1.190.3416410.28852233X-RAY DIFFRACTION31
1.19-1.230.2887800.26433635X-RAY DIFFRACTION51
1.23-1.260.29931220.25325484X-RAY DIFFRACTION77
1.26-1.30.24011280.21466953X-RAY DIFFRACTION97
1.3-1.350.21441630.19117144X-RAY DIFFRACTION100
1.35-1.40.21761510.1637192X-RAY DIFFRACTION100
1.4-1.470.17371510.14057202X-RAY DIFFRACTION100
1.47-1.540.14791740.11277168X-RAY DIFFRACTION100
1.54-1.640.1251750.09337221X-RAY DIFFRACTION100
1.64-1.770.12541570.08137249X-RAY DIFFRACTION100
1.77-1.950.10491560.08027277X-RAY DIFFRACTION100
1.95-2.230.11831340.08677336X-RAY DIFFRACTION100
2.23-2.810.12421480.1057397X-RAY DIFFRACTION100
2.81-32.150.15181450.12967739X-RAY DIFFRACTION100

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