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- PDB-8j45: Crystal structure of a Pichia pastoris-expressed IsPETase variant -

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Basic information

Entry
Database: PDB / ID: 8j45
TitleCrystal structure of a Pichia pastoris-expressed IsPETase variant
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / PET hydrolase / alpha/beta hydrolase / Ideonella Sakaiensis
Function / homology
Function and homology information


acetylesterase activity / poly(ethylene terephthalate) hydrolase / carboxylic ester hydrolase activity / 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: 1.49 Å
AuthorsLi, X. / He, H.L. / Long, X. / Niu, D. / Huang, J.-W. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Chem Eng J / Year: 2023
Title: Complete decomposition of poly(ethylene terephthalate) by crude PET hydrolytic enzyme produced in Pichia pastoris
Authors: Chen, C.C. / Li, X. / Min, J. / Zeng, Z. / Ning, Z. / He, H. / Long, X. / Niu, D. / Peng, R. / Liu, X. / Yang, Y. / Huang, J.W. / Guo, R.T.
History
DepositionApr 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Database references / Structure summary
Category: citation / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _pdbx_entry_details.has_protein_modification

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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)28,4775
Polymers27,5931
Non-polymers8854
Water6,269348
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.074, 51.271, 84.539
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 27592.625 Da / Num. of mol.: 1 / Mutation: S121E,D186H,R224Q,N233K,R280A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ideonella sakaiensis (bacteria) / Gene: ISF6_4831 / Production host: Komagataella pastoris (fungus)
References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.01 Å3/Da / Density % sol: 38.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Sodium chloride, 0.1M Sodium formate, 0.1M Bis-Tris propane pH 8.5, 25% v/v PEG Smear Medium

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Oct 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 1.49→36.21 Å / Num. obs: 35713 / % possible obs: 96.3 % / Redundancy: 11 % / Rmerge(I) obs: 0.0428 / Net I/σ(I): 38.82
Reflection shellResolution: 1.49→1.51 Å / Rmerge(I) obs: 0.0888 / Mean I/σ(I) obs: 11.47 / Num. unique obs: 1443

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SAINTdata reduction
SAINTdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→36.21 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 0.884 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16039 1766 5 %RANDOM
Rwork0.13564 ---
obs0.13688 33672 95.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.813 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.02 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 1.49→36.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1937 0 56 348 2341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132064
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171804
X-RAY DIFFRACTIONr_angle_refined_deg1.9861.6832826
X-RAY DIFFRACTIONr_angle_other_deg1.6761.6014214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6635270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.17822.13589
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.16115294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0631511
X-RAY DIFFRACTIONr_chiral_restr0.1060.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022367
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02431
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8590.8251059
X-RAY DIFFRACTIONr_mcbond_other0.8590.8241058
X-RAY DIFFRACTIONr_mcangle_it1.31.2381324
X-RAY DIFFRACTIONr_mcangle_other1.31.2391325
X-RAY DIFFRACTIONr_scbond_it1.6951.0591005
X-RAY DIFFRACTIONr_scbond_other1.6941.0621006
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5221.5331499
X-RAY DIFFRACTIONr_long_range_B_refined4.00912.1482425
X-RAY DIFFRACTIONr_long_range_B_other3.65911.1372333
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.49→1.529 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.189 135 -
Rwork0.144 2408 -
obs--93.94 %

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