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- PDB-9lmw: Crystal structure of variant FAST-ACC-T140E -

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Basic information

Entry
Database: PDB / ID: 9lmw
TitleCrystal structure of variant FAST-ACC-T140E
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

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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)27,4191
Polymers27,4191
Non-polymers00
Water6,485360
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.109, 51.394, 84.230
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: 27419.480 Da / Num. of mol.: 1 / Mutation: T140E
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.: 360 / 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: 2.02 Å3/Da / Density % sol: 39.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.5 M (NH4)2SO4, 0.1 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: Oct 5, 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: 36232 / % possible obs: 99.7 % / Redundancy: 5.7 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.018 / Rrim(I) all: 0.044 / Χ2: 1.036 / Net I/σ(I): 24.5 / Num. measured all: 206254
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.5-1.555.30.04135610.9980.9990.020.0460.7999.9
1.55-1.6250.03835830.9980.9990.020.0430.79899.8
1.62-1.695.50.03735520.9980.9990.0180.0420.83399.8
1.69-1.785.30.03535850.99810.0170.0390.8699.8
1.78-1.895.80.03435830.99810.0160.0380.91499.7
1.89-2.045.90.03435920.99810.0160.0371.04699.6
2.04-2.2460.03436330.99910.0150.0371.179100
2.24-2.5660.03436370.9980.9990.0150.0371.224100
2.56-3.2360.03936790.9960.9990.0180.0431.15399.8
3.23-2560.0538270.9950.9990.0230.0551.39298.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
HKL-2000data reduction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→24.65 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 0.824 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16436 1779 4.9 %RANDOM
Rwork0.13264 ---
obs0.1342 34396 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 4.712 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.5→24.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1922 0 0 361 2283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131989
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171744
X-RAY DIFFRACTIONr_angle_refined_deg1.9311.6392719
X-RAY DIFFRACTIONr_angle_other_deg1.7051.5634069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7695270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.18222.06987
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.90915288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2371511
X-RAY DIFFRACTIONr_chiral_restr0.1040.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022308
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_it0.6140.3341059
X-RAY DIFFRACTIONr_mcbond_other0.6140.3331058
X-RAY DIFFRACTIONr_mcangle_it1.0150.51324
X-RAY DIFFRACTIONr_mcangle_other1.0150.51325
X-RAY DIFFRACTIONr_scbond_it1.1510.404930
X-RAY DIFFRACTIONr_scbond_other1.1490.403929
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7030.5731391
X-RAY DIFFRACTIONr_long_range_B_refined3.7895.2422333
X-RAY DIFFRACTIONr_long_range_B_other3.1444.3062244
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.154 100 -
Rwork0.129 2525 -
obs--99.58 %

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