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- PDB-7vwn: The structure of an engineered PET hydrolase -

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Basic information

Entry
Database: PDB / ID: 7vwn
TitleThe structure of an engineered PET hydrolase
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / PET hydrolase / PETase / biodegradation of microplastics
Function / homology
Function and homology information


poly(ethylene terephthalate) hydrolase / acetylesterase activity / carboxylic ester hydrolase activity / cellular response to organic substance / xenobiotic catabolic process / extracellular region
Similarity search - Function
Dienelactone hydrolase / Dienelactone hydrolase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Poly(ethylene terephthalate) hydrolase
Similarity search - Component
Biological speciesIdeonella sakaiensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsXie, W. / Jia, Q.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770075 China
National Natural Science Foundation of China (NSFC)31870782 China
CitationJournal: To Be Published
Title: An engineered PET hydrolase for biodegradation of microplastics in ocean water
Authors: Xie, W. / Jia, Q.
History
DepositionNov 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6224
Polymers28,5161
Non-polymers1063
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, PDBePISA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-10 kcal/mol
Surface area9610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.588, 50.536, 41.370
Angle α, β, γ (deg.)90.000, 92.458, 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
Components on special symmetry positions
IDModelComponents
11A-644-

HOH

21A-662-

HOH

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Components

#1: Protein Poly(ethylene terephthalate) hydrolase / PET hydrolase / PETase / PET-digesting enzyme


Mass: 28515.600 Da / Num. of mol.: 1
Mutation: T29S, K95N, I168R, P181V, S214V, N233C, A248D, R280A, S282C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ideonella sakaiensis (strain NBRC 110686 / TISTR 2288 / 201-F6) (bacteria)
Strain: NBRC 110686 / TISTR 2288 / 201-F6 / Gene: ISF6_4831 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 41.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 1.8 M (NH4)2SO4, 0.1 M NaCl and 0.1 M MES pH6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 0.979 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Jul 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 42326 / % possible obs: 98.2 % / Redundancy: 6.7 % / Biso Wilson estimate: 15.37 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.063 / Net I/σ(I): 23.3
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 3822 / CC1/2: 0.93 / % possible all: 91

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EQE

6eqe


Resolution: 1.45→32.95 Å / SU ML: 0.1257 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.4513 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1788 2165 5.21 %
Rwork0.1546 39383 -
obs0.1559 41548 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.81 Å2
Refinement stepCycle: LAST / Resolution: 1.45→32.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1924 0 3 282 2209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01381985
X-RAY DIFFRACTIONf_angle_d1.39242711
X-RAY DIFFRACTIONf_chiral_restr0.1236300
X-RAY DIFFRACTIONf_plane_restr0.0108359
X-RAY DIFFRACTIONf_dihedral_angle_d3.9691102
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.490.25551330.2172490X-RAY DIFFRACTION93.54
1.49-1.520.25271410.19842582X-RAY DIFFRACTION97.88
1.52-1.560.22521610.18592576X-RAY DIFFRACTION98.03
1.56-1.610.22741420.1872591X-RAY DIFFRACTION98.24
1.61-1.660.20141550.17962603X-RAY DIFFRACTION98.32
1.66-1.720.19851330.1752629X-RAY DIFFRACTION98.61
1.72-1.790.2111310.16422615X-RAY DIFFRACTION98.56
1.79-1.870.18531480.15882624X-RAY DIFFRACTION98.58
1.87-1.970.18711400.15832639X-RAY DIFFRACTION99.29
1.97-2.10.16851390.15182629X-RAY DIFFRACTION99.28
2.1-2.260.1811370.14962668X-RAY DIFFRACTION99.4
2.26-2.480.16171490.14982639X-RAY DIFFRACTION99.61
2.48-2.840.15851470.14942691X-RAY DIFFRACTION99.82
2.84-3.580.16171570.14242654X-RAY DIFFRACTION100
3.58-32.950.1751520.14492753X-RAY DIFFRACTION99.86
Refinement TLS params.Method: refined / Origin x: 17.3142520429 Å / Origin y: 0.0269757496878 Å / Origin z: 11.5592270117 Å
111213212223313233
T0.132784956294 Å20.0204926882239 Å20.00763590103791 Å2-0.115115145907 Å2-0.00715248473477 Å2--0.0771075621616 Å2
L2.57405549597 °2-0.20231613674 °20.437118967333 °2-1.39502521359 °2-0.108752919334 °2--1.14899065147 °2
S0.0625707164727 Å °0.332457780433 Å °-0.0259774994391 Å °-0.234830377828 Å °-0.059580382937 Å °0.019926616975 Å °-0.0372877100568 Å °-0.0402335067127 Å °-0.00803150598201 Å °
Refinement TLS groupSelection details: all

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