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- PDB-9qva: Polyester Hydrolase Leipzig 7 (PHL7) variant R2M2-P155G-A186S -

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Basic information

Entry
Database: PDB / ID: 9qva
TitlePolyester Hydrolase Leipzig 7 (PHL7) variant R2M2-P155G-A186S
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 / FOURIER SYNTHESIS / Resolution: 1.59 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 11, 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)58,0724
Polymers57,6882
Non-polymers3842
Water12,574698
1
A: Polyester Hydrolase Leipzig 7 (PHL-7), catalysis-deficient S131A mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0362
Polymers28,8441
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)29,0362
Polymers28,8441
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.610, 74.056, 63.503
Angle α, β, γ (deg.)90.000, 97.570, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 2 through 13 or resid 15...
d_2ens_1(chain "B" and (resid 2 through 13 or resid 15...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALAGLUGLUAA2 - 132 - 13
d_12SERSERVALVALAA15 - 1915 - 19
d_13GLYGLYALAALAAA21 - 2421 - 24
d_14ALAALAVALVALAA26 - 3026 - 30
d_15ARGARGLEULEUAA32 - 10332 - 103
d_16ALAALAVALVALAA105 - 116105 - 116
d_17ARGARGLEULEUAA119 - 138119 - 138
d_18ALAALAASNASNAA140 - 143140 - 143
d_19PROPROPROPROAA145145
d_110LEULEUVALVALAA147 - 165147 - 165
d_111VALVALTHRTHRAA167 - 178167 - 178
d_112ALAALASERSERAA180 - 186180 - 186
d_113ALAALAASNASNAA188 - 191188 - 191
d_114LEULEUPROPROAA193 - 194193 - 194
d_115SERSERVALVALAA196 - 211196 - 211
d_116ASNASNASNASNAA213213
d_117PROPROSERSERAA215 - 251215 - 251
d_118TYRTYRGLUGLUAA253 - 261253 - 261
d_119CITCITCITCITAC301
d_21ALAALAGLUGLUBB2 - 132 - 13
d_22SERSERVALVALBB15 - 1915 - 19
d_23GLYGLYALAALABB21 - 2421 - 24
d_24ALAALAVALVALBB26 - 3026 - 30
d_25ARGARGLEULEUBB32 - 10332 - 103
d_26ALAALAVALVALBB105 - 116105 - 116
d_27ARGARGLEULEUBB119 - 138119 - 138
d_28ALAALAASNASNBB140 - 143140 - 143
d_29PROPROPROPROBB145145
d_210LEULEUVALVALBB147 - 165147 - 165
d_211VALVALTHRTHRBB167 - 178167 - 178
d_212ALAALASERSERBB180 - 186180 - 186
d_213ALAALAASNASNBB188 - 191188 - 191
d_214LEULEUPROPROBB193 - 194193 - 194
d_215SERSERVALVALBB196 - 211196 - 211
d_216ASNASNASNASNBB213213
d_217PROPROSERSERBB215 - 251215 - 251
d_218TYRTYRGLUGLUBB253 - 261253 - 261
d_219CITCITCITCITBD301

NCS oper: (Code: givenMatrix: (0.964989988383, -0.000919836725696, 0.262285104841), (-0.00172735969294, -0.999994451839, 0.0028482486193), (0.262281029717, -0.00320159212021, -0.964986223352)Vector: - ...NCS oper: (Code: given
Matrix: (0.964989988383, -0.000919836725696, 0.262285104841), (-0.00172735969294, -0.999994451839, 0.0028482486193), (0.262281029717, -0.00320159212021, -0.964986223352)
Vector: -3.11121990021, 17.5972082477, 24.73915487)

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Components

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


Mass: 28844.121 Da / Num. of mol.: 2
Mutation: E6Q, Q34D, D36S, E68S, T91S, Q104L, H109Y, R111T, N113D, V115T, N118D, A131S, T145P, E148K, P155G, N161D, T167V, V171I, A186S, D196S, D198P, S208D, D216N, L235T, F248P
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.: 698 / 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: 2.13 Å3/Da / Density % sol: 42.14 %
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: P14 (MX2) / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.59→62.95 Å / Num. obs: 72371 / % possible obs: 90.6 % / Redundancy: 7 % / Biso Wilson estimate: 11.93 Å2 / CC1/2: 0.994 / Net I/σ(I): 6.9
Reflection shellResolution: 1.59→1.75 Å / Num. unique obs: 1847 / CC1/2: 0.587

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Processing

Software
NameVersionClassification
REFMAC8refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.59→62.95 Å / SU ML: 0.2163 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.3113
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2461 4002 5.53 %
Rwork0.2007 68369 -
obs0.2032 72371 56.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.19 Å2
Refinement stepCycle: LAST / Resolution: 1.59→62.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3946 0 26 704 4676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00184240
X-RAY DIFFRACTIONf_angle_d0.48255840
X-RAY DIFFRACTIONf_chiral_restr0.0422653
X-RAY DIFFRACTIONf_plane_restr0.0047781
X-RAY DIFFRACTIONf_dihedral_angle_d10.50041572
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.72602242511 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.610.31782X-RAY DIFFRACTION
1.61-1.630.4048130.3135171X-RAY DIFFRACTION
1.63-1.650.195613271X-RAY DIFFRACTION
1.65-1.670.3517230.2462467X-RAY DIFFRACTION
1.67-1.690.3097470.2582578X-RAY DIFFRACTION
1.69-1.710.3348430.2946758X-RAY DIFFRACTION
1.72-1.740.3226550.2844853X-RAY DIFFRACTION20.85
1.74-1.770.3371720.28611032X-RAY DIFFRACTION25.05
1.77-1.80.3523830.27811175X-RAY DIFFRACTION28.4
1.8-1.830.3452780.28751348X-RAY DIFFRACTION32.31
1.83-1.860.2481020.27061495X-RAY DIFFRACTION36.12
1.86-1.90.3011920.26821663X-RAY DIFFRACTION39.27
1.9-1.940.29821180.25771790X-RAY DIFFRACTION43.56
1.94-1.980.22161080.24322088X-RAY DIFFRACTION49.48
1.98-2.020.28041220.2422279X-RAY DIFFRACTION54.05
2.02-2.070.30491370.24032573X-RAY DIFFRACTION61.62
2.07-2.130.30981570.23262884X-RAY DIFFRACTION68.85
2.13-2.190.25461790.22033159X-RAY DIFFRACTION74.88
2.19-2.260.29181720.21323391X-RAY DIFFRACTION80.74
2.26-2.340.2662180.2113598X-RAY DIFFRACTION86.77
2.34-2.440.27152180.2133944X-RAY DIFFRACTION93.51
2.44-2.550.24582980.21684033X-RAY DIFFRACTION98.14
2.55-2.680.21412490.21044102X-RAY DIFFRACTION98.19
2.68-2.850.25822400.20263993X-RAY DIFFRACTION96.07
2.85-3.070.25692220.18774072X-RAY DIFFRACTION96.41
3.07-3.380.21882750.17174109X-RAY DIFFRACTION99.46
3.38-3.870.19132120.15444206X-RAY DIFFRACTION99.66
3.87-4.870.2032240.15014193X-RAY DIFFRACTION99.35
4.88-62.950.24692320.21564062X-RAY DIFFRACTION97.19

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