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- PDB-9hl5: Crystal structure of halo-tolerant PETase from marine metagenome ... -

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Basic information

Entry
Database: PDB / ID: 9hl5
TitleCrystal structure of halo-tolerant PETase from marine metagenome (HaloPETase1)
ComponentsAlpha/beta hydrolase
KeywordsHYDROLASE / PETase / halo-tolerant / HaloPETase / HaloPETase1 / polyesterase / marine / metagenome
Function / homologyDI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsTurak, O. / Kriegel, M. / Hocker, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Protein Sci. / Year: 2025
Title: A third type of PETase from the marine Halopseudomonas lineage.
Authors: Turak, O. / Gagsteiger, A. / Upadhyay, A. / Kriegel, M. / Salein, P. / Bohnke-Brandt, S. / Agarwal, S. / Borchert, E. / Hocker, B.
History
DepositionDec 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,77231
Polymers27,7851
Non-polymers2,98730
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint56 kcal/mol
Surface area10420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.340, 70.530, 72.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha/beta hydrolase


Mass: 27785.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: first (1, S) and last (270, A) amino acids are from FX-cloning.
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: BXT89_15940 / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 215 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M imidazole, 40 % (v/v) PEG400

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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: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.16→35.27 Å / Num. obs: 93276 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 8.77 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06117 / Net I/σ(I): 15.86
Reflection shellResolution: 1.16→1.19 Å / Mean I/σ(I) obs: 4.17 / Num. unique obs: 6131 / CC1/2: 0.929 / % possible all: 99.79

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Processing

Software
NameVersionClassification
PHENIX1.21.1-5286refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.16→35.27 Å / SU ML: 0.0687 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 10.1904
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1289 2092 2.24 %
Rwork0.1098 91179 -
obs0.1103 93271 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.38 Å2
Refinement stepCycle: LAST / Resolution: 1.16→35.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1954 0 196 185 2335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00692256
X-RAY DIFFRACTIONf_angle_d1.05933020
X-RAY DIFFRACTIONf_chiral_restr0.0888309
X-RAY DIFFRACTIONf_plane_restr0.0107388
X-RAY DIFFRACTIONf_dihedral_angle_d14.5758832
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.16-1.190.1511370.14475994X-RAY DIFFRACTION99.79
1.19-1.220.15711390.13686015X-RAY DIFFRACTION99.94
1.22-1.250.1491380.12576003X-RAY DIFFRACTION99.89
1.25-1.290.16081360.11935984X-RAY DIFFRACTION99.85
1.29-1.330.13741390.10926034X-RAY DIFFRACTION99.9
1.33-1.380.1091380.09616040X-RAY DIFFRACTION99.98
1.38-1.430.12381370.09156007X-RAY DIFFRACTION99.97
1.43-1.50.10851400.08236076X-RAY DIFFRACTION99.94
1.5-1.570.10411390.07776047X-RAY DIFFRACTION99.97
1.57-1.670.10111390.07896072X-RAY DIFFRACTION99.98
1.67-1.80.10771400.08256093X-RAY DIFFRACTION99.98
1.8-1.980.10991400.08316087X-RAY DIFFRACTION99.98
1.98-2.270.10171410.08736138X-RAY DIFFRACTION99.98
2.27-2.860.11621420.10996177X-RAY DIFFRACTION99.95
2.86-35.270.16641470.15126412X-RAY DIFFRACTION99.77

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