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- PDB-9lmt: Crystal structure of variant FAST-ACC-A248E -

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Basic information

Entry
Database: PDB / ID: 9lmt
TitleCrystal structure of variant FAST-ACC-A248E
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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

Downloads & links

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Assembly

Deposited unit
A: Poly(ethylene terephthalate) hydrolase


Theoretical massNumber of molelcules
Total (without water)27,3921
Polymers27,3921
Non-polymers00
Water5,747319
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.026, 51.610, 84.496
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: 27392.455 Da / Num. of mol.: 1 / Mutation: A248E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Piscinibacter sakaiensis (bacteria) / Gene: ISF6_4831 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.03 Å3/Da / Density % sol: 39.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: 1 M (NH4)2SO4, 0.15 M NaCl, 0.1 M Bis-Tris, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.5→25 Å / Num. obs: 36009 / % possible obs: 98.4 % / Redundancy: 4.6 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.019 / Rrim(I) all: 0.042 / Χ2: 1.204 / Net I/σ(I): 35.7 / Num. measured all: 166988
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.5-1.554.40.05835280.9950.9990.0330.0671.3298.4
1.55-1.624.50.05435830.9940.9990.030.0631.28798.7
1.62-1.694.20.05135170.9960.9990.0290.0591.26698.1
1.69-1.784.70.04735640.9960.9990.0250.0531.2198.8
1.78-1.894.60.04435740.9960.9990.0240.0511.3498.8
1.89-2.044.60.04135800.9970.9990.0220.0471.27898.7
2.04-2.244.60.03836100.9970.9990.020.0431.19198.4
2.24-2.564.40.03736040.9970.9990.020.0421.07398.3
2.56-3.234.90.03636430.9980.9990.0180.041.00498.1
3.23-255.40.03338060.99910.0150.0361.12897.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→25 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 0.857 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16247 1767 4.9 %RANDOM
Rwork0.13355 ---
obs0.13498 34189 98.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 5.604 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0 Å20 Å2
2--0.24 Å2-0 Å2
3----0.12 Å2
Refinement stepCycle: 1 / Resolution: 1.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1920 0 0 319 2239
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131989
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171738
X-RAY DIFFRACTIONr_angle_refined_deg1.9831.642721
X-RAY DIFFRACTIONr_angle_other_deg1.7011.5634059
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6065271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.58622.06987
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.53615289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9791511
X-RAY DIFFRACTIONr_chiral_restr0.1090.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022308
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02417
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_it0.690.4111057
X-RAY DIFFRACTIONr_mcbond_other0.6870.411056
X-RAY DIFFRACTIONr_mcangle_it1.0940.6161322
X-RAY DIFFRACTIONr_mcangle_other1.0930.6171323
X-RAY DIFFRACTIONr_scbond_it1.5940.536932
X-RAY DIFFRACTIONr_scbond_other1.5910.535931
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3110.7531394
X-RAY DIFFRACTIONr_long_range_B_refined4.0856.1472299
X-RAY DIFFRACTIONr_long_range_B_other3.6985.4272230
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.537 Å
RfactorNum. reflection% reflection
Rfree0.18 106 -
Rwork0.141 2425 -
obs--94.97 %

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