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- PDB-9qdv: Crystal structure of the polyester hydrolase Leipzig 7 (PHL7) mut... -

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Basic information

Entry
Database: PDB / ID: 9qdv
TitleCrystal structure of the polyester hydrolase Leipzig 7 (PHL7) mut3 variant expressed in E. coli (E_PHL7mut3)
ComponentsPolyester Hydrolase Leipzig 7 (PHL-7), catalysis-deficient S131A mutant
KeywordsHYDROLASE / E. coli / LCC / K. phaffii / PETase / P. pastoris
Function / homologyCutinase / PET hydrolase-like / : / hydrolase activity, acting on ester bonds / Alpha/Beta hydrolase fold / 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: 0.89 Å
AuthorsUseini, A. / Strater, N. / Striedner, G. / Sonnendecker, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)European Union's Horizon 2020 research and inovation, grant number 887913 (Enzycle)European Union
CitationJournal: ACS ES T Eng / Year: 2025
Title: Trade-Offs between Stability and Activity of Glycosylated and Non-Glycosylated Polyester Hydrolases PHL7 and PHL7mut3
Authors: Fohler, L. / Faschingeder, F. / Leibetseder, L. / Zhao, Z. / Useini, A. / Strater, N. / Sonnendecker, C. / Ewing, T.A. / Moers, A.P.H.A. / Werten, M.W.T. / van Vliet, D.M. / Julsing, M.K. / ...Authors: Fohler, L. / Faschingeder, F. / Leibetseder, L. / Zhao, Z. / Useini, A. / Strater, N. / Sonnendecker, C. / Ewing, T.A. / Moers, A.P.H.A. / Werten, M.W.T. / van Vliet, D.M. / Julsing, M.K. / Zimmermann, W. / Striedner, G.
History
DepositionMar 7, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 10, 2025Provider: 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


Theoretical massNumber of molelcules
Total (without water)58,1192
Polymers58,1192
Non-polymers00
Water15,133840
1
A: Polyester Hydrolase Leipzig 7 (PHL-7), catalysis-deficient S131A mutant


Theoretical massNumber of molelcules
Total (without water)29,0591
Polymers29,0591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polyester Hydrolase Leipzig 7 (PHL-7), catalysis-deficient S131A mutant


Theoretical massNumber of molelcules
Total (without water)29,0591
Polymers29,0591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.441, 43.902, 100.123
Angle α, β, γ (deg.)90.000, 130.867, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 29059.285 Da / Num. of mol.: 2 / Mutation: Q175E, L210T, D233K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) compost metagenome (others) / Production host: Escherichia coli (E. coli) / References: UniProt: A0AA82WPD4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 840 / Source method: isolated from a natural source / Formula: H2O
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: 2.15 Å3/Da / Density % sol: 42.82 %
Crystal growTemperature: 292 K / Method: vapor diffusion / Details: 0.2 M NaCl, 0.1 M HEPES, pH 7.5, 25% w/v PEG 3350

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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: 0.73 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.73 Å / Relative weight: 1
ReflectionResolution: 0.89→75.72 Å / Num. obs: 292736 / % possible obs: 92.5 % / Redundancy: 6.9 % / Biso Wilson estimate: 8.53 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.5
Reflection shellResolution: 0.89→0.96 Å / Num. unique obs: 14640 / CC1/2: 0.633

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.89→32.93 Å / SU ML: 0.071 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.6807
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.131 5774 0.98 %
Rwork0.1186 581976 -
obs0.1187 292736 80.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.45 Å2
Refinement stepCycle: LAST / Resolution: 0.89→32.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3938 0 0 840 4778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00954327
X-RAY DIFFRACTIONf_angle_d1.20535944
X-RAY DIFFRACTIONf_chiral_restr0.0893653
X-RAY DIFFRACTIONf_plane_restr0.0147804
X-RAY DIFFRACTIONf_dihedral_angle_d12.59311594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.89-0.90.2593200.26081099X-RAY DIFFRACTION4.61
0.9-0.910.3284140.26332215X-RAY DIFFRACTION9.13
0.91-0.930.2718300.2583856X-RAY DIFFRACTION15.91
0.93-0.940.2782900.26356345X-RAY DIFFRACTION26.45
0.94-0.950.2528990.25839489X-RAY DIFFRACTION39.19
0.95-0.960.24891100.250512187X-RAY DIFFRACTION50.51
0.96-0.980.29261250.248314577X-RAY DIFFRACTION59.84
0.98-0.990.24291680.23516316X-RAY DIFFRACTION67.46
0.99-1.010.22521780.214518246X-RAY DIFFRACTION75.59
1.01-1.020.22342370.198719962X-RAY DIFFRACTION82.8
1.02-1.040.22262590.187621732X-RAY DIFFRACTION89.72
1.04-1.060.17272210.180823006X-RAY DIFFRACTION95.24
1.06-1.080.19152450.164623926X-RAY DIFFRACTION99.15
1.08-1.10.16432550.148224150X-RAY DIFFRACTION99.78
1.1-1.130.15542440.134924102X-RAY DIFFRACTION99.59
1.13-1.150.14462920.124724087X-RAY DIFFRACTION99.58
1.15-1.180.12582490.117323947X-RAY DIFFRACTION99.48
1.18-1.210.14742220.111424007X-RAY DIFFRACTION99.27
1.21-1.250.13051860.109624049X-RAY DIFFRACTION99.06
1.25-1.290.13052160.107123780X-RAY DIFFRACTION98.11
1.29-1.340.13922160.100723748X-RAY DIFFRACTION98.2
1.34-1.390.11372450.09824150X-RAY DIFFRACTION99.93
1.39-1.450.10872180.094524272X-RAY DIFFRACTION99.93
1.45-1.530.10772760.091924088X-RAY DIFFRACTION99.88
1.53-1.620.09082150.093124231X-RAY DIFFRACTION99.92
1.62-1.750.11972240.098824165X-RAY DIFFRACTION99.89
1.75-1.930.1062530.104424071X-RAY DIFFRACTION99.82
1.93-2.20.10092010.108124169X-RAY DIFFRACTION99.49
2.2-2.780.12942880.11323841X-RAY DIFFRACTION98.83
2.78-32.930.12811780.120324163X-RAY DIFFRACTION99.66

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