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- PDB-9lmx: Inactive mutant of FAST-ACC-T140E/R132G in complex with mono(2-hy... -

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Basic information

Entry
Database: PDB / ID: 9lmx
TitleInactive mutant of FAST-ACC-T140E/R132G in complex with mono(2-hydroxyethyl) terephthalic acid
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
4-(2-hydroxyethyloxycarbonyl)benzoic acid / Poly(ethylene terephthalate) hydrolase
Similarity search - Component
Biological speciesPiscinibacter sakaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5142
Polymers27,3031
Non-polymers2101
Water4,810267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.813, 51.209, 84.104
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: 27303.340 Da / Num. of mol.: 1 / Mutation: R132G,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: Chemical ChemComp-C9C / 4-(2-hydroxyethyloxycarbonyl)benzoic acid / monohydroxyethyl terephthalate


Mass: 210.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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 Å3/Da / Density % sol: 38.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.2 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 07A / Wavelength: 0.97621 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Dec 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97621 Å / Relative weight: 1
ReflectionResolution: 1.4→25 Å / Num. obs: 43357 / % possible obs: 98.3 % / Redundancy: 4.8 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.025 / Rrim(I) all: 0.054 / Χ2: 1.264 / Net I/σ(I): 30.8 / Num. measured all: 206942
Reflection shell

CC star: 0.999 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.454.90.05941930.9940.0310.0671.26696.3
1.45-1.514.80.05642890.9950.0290.0631.27698.3
1.51-1.584.90.05442690.9950.0280.0611.26898.8
1.58-1.664.80.05343080.9950.0280.061.30398.8
1.66-1.764.80.05243360.9950.0270.0591.31598.9
1.76-1.94.60.0543230.9950.0270.0571.32198.8
1.9-2.094.80.04943060.9950.0250.0551.27698.2
2.09-2.394.90.04743870.9960.0240.0531.22499.4
2.39-3.014.80.04744480.9960.0240.0531.20799.1
3.01-254.40.04644980.9950.0250.0531.18296.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→24.6 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.163 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14169 2220 5.1 %RANDOM
Rwork0.10752 ---
obs0.10927 41082 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.839 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20 Å2
2--0.23 Å2-0 Å2
3----0.69 Å2
Refinement stepCycle: 1 / Resolution: 1.4→24.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1914 0 15 267 2196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131994
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171736
X-RAY DIFFRACTIONr_angle_refined_deg1.7741.6472725
X-RAY DIFFRACTIONr_angle_other_deg1.681.5714052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6075270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11622.35385
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.29215283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9081510
X-RAY DIFFRACTIONr_chiral_restr0.1030.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022318
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02416
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_it1.2470.7471059
X-RAY DIFFRACTIONr_mcbond_other1.2460.7461058
X-RAY DIFFRACTIONr_mcangle_it1.6121.131324
X-RAY DIFFRACTIONr_mcangle_other1.6111.131325
X-RAY DIFFRACTIONr_scbond_it1.7650.918935
X-RAY DIFFRACTIONr_scbond_other1.7540.918935
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2021.311398
X-RAY DIFFRACTIONr_long_range_B_refined2.71310.2092299
X-RAY DIFFRACTIONr_long_range_B_other2.4829.6982253
X-RAY DIFFRACTIONr_rigid_bond_restr1.93433730
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.435 Å
RfactorNum. reflection% reflection
Rfree0.148 172 -
Rwork0.074 2854 -
obs--94.21 %

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