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- PDB-9lms: Crystal structure of Pichia pastoris-expressed FAST-PETase-N212A/... -

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Basic information

Entry
Database: PDB / ID: 9lms
TitleCrystal structure of Pichia pastoris-expressed FAST-PETase-N212A/K233C/S282C variant
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / PET hydrolase / PET degradation enzyme
Function / homology
Function and homology information


acetylesterase activity / poly(ethylene terephthalate) hydrolase / carboxylic ester hydrolase activity / xenobiotic catabolic process / extracellular region
Similarity search - Function
Cutinase / PET hydrolase-like / : / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Poly(ethylene terephthalate) hydrolase
Similarity search - Component
Biological speciesPiscinibacter sakaiensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsLi, X. / Ning, Z.Y. / Huang, S.Q. / Zeng, C. / Zeng, Z.Y. / Ji, R. / Huang, J.-W. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Combined approaches to enhance the Pichia pastoris-expressed PET hydrolase.
Authors: Li, X. / Huang, J.W. / Ning, Z. / Huang, S. / Zeng, C. / Zeng, Z. / Ji, R. / Peng, R. / Liu, X. / Min, J. / Chen, C.C. / Guo, R.T.
History
DepositionJan 20, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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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)28,2955
Polymers27,4111
Non-polymers8854
Water4,360242
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.000, 51.018, 83.971
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: 27410.516 Da / Num. of mol.: 1 / Mutation: N212A,N233C,S282C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Piscinibacter 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.: 242 / 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: 1.99 Å3/Da / Density % sol: 38.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: 25% PEG 1500, 0.1 M MMT, pH 9.0

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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 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 1.71→33.16 Å / Num. obs: 24277 / % possible obs: 99.5 % / Redundancy: 8.76 % / Rmerge(I) obs: 0.0337 / Net I/σ(I): 40.32
Reflection shellResolution: 1.71→1.81 Å / Redundancy: 3.89 % / Rmerge(I) obs: 0.0674 / Num. unique obs: 1176 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SAINTdata scaling
SAINTdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→33.16 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.603 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17129 1190 4.9 %RANDOM
Rwork0.13816 ---
obs0.13977 22997 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2--0.12 Å2-0 Å2
3----0.25 Å2
Refinement stepCycle: 1 / Resolution: 1.71→33.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1922 0 56 242 2220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132054
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181785
X-RAY DIFFRACTIONr_angle_refined_deg1.951.6822816
X-RAY DIFFRACTIONr_angle_other_deg1.6571.64172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0425271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.01522.04588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87715288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9941511
X-RAY DIFFRACTIONr_chiral_restr0.1030.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022363
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02430
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_it1.0271.0621057
X-RAY DIFFRACTIONr_mcbond_other1.0271.0611056
X-RAY DIFFRACTIONr_mcangle_it1.5391.5891322
X-RAY DIFFRACTIONr_mcangle_other1.5381.591323
X-RAY DIFFRACTIONr_scbond_it1.8961.382997
X-RAY DIFFRACTIONr_scbond_other1.8961.386998
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.852.0061490
X-RAY DIFFRACTIONr_long_range_B_refined3.99314.4822344
X-RAY DIFFRACTIONr_long_range_B_other3.814.1412302
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.71→1.754 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 94 -
Rwork0.154 1663 -
obs--98.82 %

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