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- PDB-9qnm: Polyester Hydrolase Leipzig 7 (PHL7) variant R2M2 -

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Basic information

Entry
Database: PDB / ID: 9qnm
TitlePolyester Hydrolase Leipzig 7 (PHL7) variant R2M2
ComponentsPolyester Hydrolase Leipzig 7 (PHL-7), catalysis-deficient S131A mutant
KeywordsHYDROLASE / PET hydrolase / enzymatic plastic degradation / enzyme engineering / Polyester Hydrolase Leipzig 7
Function / homologyCutinase / PET hydrolase-like / : / hydrolase activity, acting on ester bonds / Alpha/Beta hydrolase fold / metal ion binding / CITRIC ACID / 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: 1.12 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
DepositionMar 25, 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 (PHL-7), catalysis-deficient S131A mutant
B: Polyester Hydrolase Leipzig 7 (PHL-7), catalysis-deficient S131A mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1214
Polymers57,7362
Non-polymers3842
Water13,637757
1
A: Polyester Hydrolase Leipzig 7 (PHL-7), catalysis-deficient S131A mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0602
Polymers28,8681
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polyester Hydrolase Leipzig 7 (PHL-7), catalysis-deficient S131A mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0602
Polymers28,8681
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.260, 74.096, 63.596
Angle α, β, γ (deg.)90.00, 97.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 28868.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) compost metagenome (others) / Production host: Escherichia coli (E. coli) / References: UniProt: A0AA82WPD4
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 757 / 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: 2.12 Å3/Da / Density % sol: 41.87 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate pH 4.0, 10% (w/v) PEG 6000, 3% (v/v) 1,6-hexanediol

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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: Jul 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.12→63.1 Å / Num. obs: 99522 / % possible obs: 90.8 % / Redundancy: 6.7 % / CC1/2: 0.999 / Net I/σ(I): 10.6
Reflection shellResolution: 1.12→1.24 Å / Num. unique obs: 4977 / CC1/2: 0.578

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.12→63.1 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2025 5041 2.57 %
Rwork0.1721 --
obs0.1729 99522 53.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.12→63.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3950 0 26 760 4736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.025
X-RAY DIFFRACTIONf_dihedral_angle_d11.4451561
X-RAY DIFFRACTIONf_chiral_restr0.083651
X-RAY DIFFRACTIONf_plane_restr0.013775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.12-1.130.562180.2901203X-RAY DIFFRACTION
1.13-1.1400.3187400X-RAY DIFFRACTION3
1.14-1.160.3456120.2708674X-RAY DIFFRACTION6
1.16-1.170.262240.25551016X-RAY DIFFRACTION9
1.17-1.190.2167300.25291319X-RAY DIFFRACTION11
1.19-1.20.2997310.2661643X-RAY DIFFRACTION14
1.2-1.220.2532500.25962053X-RAY DIFFRACTION17
1.22-1.240.3703500.252534X-RAY DIFFRACTION21
1.24-1.260.3421700.24942980X-RAY DIFFRACTION25
1.26-1.280.2791900.25383436X-RAY DIFFRACTION29
1.28-1.30.26771060.25413907X-RAY DIFFRACTION33
1.3-1.330.24231110.23884289X-RAY DIFFRACTION36
1.33-1.350.2441340.24484637X-RAY DIFFRACTION39
1.35-1.380.23251450.23945163X-RAY DIFFRACTION43
1.38-1.410.23861750.22725715X-RAY DIFFRACTION48
1.41-1.440.24481630.22116397X-RAY DIFFRACTION54
1.44-1.480.23872150.22027123X-RAY DIFFRACTION60
1.48-1.520.24882150.2127868X-RAY DIFFRACTION66
1.52-1.560.23882240.2068666X-RAY DIFFRACTION73
1.56-1.610.23072580.20239593X-RAY DIFFRACTION81
1.61-1.670.20352710.190710434X-RAY DIFFRACTION88
1.67-1.740.20352570.193611147X-RAY DIFFRACTION94
1.74-1.820.22763010.184311687X-RAY DIFFRACTION98
1.82-1.910.20383300.167411675X-RAY DIFFRACTION99
1.91-2.030.17662510.146710534X-RAY DIFFRACTION89
2.03-2.190.1822860.146710883X-RAY DIFFRACTION91
2.19-2.410.1772560.14469649X-RAY DIFFRACTION81
2.41-2.760.18373420.15911853X-RAY DIFFRACTION100
2.76-3.470.18873350.156611713X-RAY DIFFRACTION99
3.47-63.10.19763010.159611850X-RAY DIFFRACTION100

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