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- PDB-9lmv: Crystal structure of FAST-ACC-T140D/R132G/S160A mutant in complex... -

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Basic information

Entry
Database: PDB / ID: 9lmv
TitleCrystal structure of FAST-ACC-T140D/R132G/S160A mutant 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: 1.57 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

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Assembly

Deposited unit
A: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4992
Polymers27,2891
Non-polymers2101
Water5,260292
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.852, 50.961, 83.969
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: 27289.312 Da / Num. of mol.: 1 / Mutation: R132G,T140D,S160A
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.: 292 / 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: 1.99 Å3/Da / Density % sol: 38.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.3 M (NH4)2SO4, 0.2 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 EIGER 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: 1.57→25 Å / Num. obs: 29953 / % possible obs: 95.9 % / Redundancy: 5.2 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.022 / Rrim(I) all: 0.052 / Χ2: 1.243 / Net I/σ(I): 29.2 / Num. measured all: 155392
Reflection shell

CC star: 0.999 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.57-1.635.40.05129490.9970.0240.0561.39195.7
1.63-1.695.20.0529430.9960.0240.0561.2196
1.69-1.775.20.04929590.9950.0240.0551.19796.6
1.77-1.865.10.04729760.9960.0230.0531.2296.5
1.86-1.984.90.04729410.9960.0230.0521.25495.2
1.98-2.135.30.04530210.9960.0220.051.31696.8
2.13-2.345.30.04430300.9970.0210.0491.29397.7
2.34-2.685.20.04430440.9960.0210.0491.32796.9
2.68-3.385.20.04530570.9960.0210.051.06796.1
3.38-2550.04830330.9960.0230.0541.14391.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→24.54 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.986 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14962 1424 4.8 %RANDOM
Rwork0.09765 ---
obs0.10011 28498 95.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.078 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0 Å20 Å2
2--0.39 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.57→24.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1913 0 15 292 2220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0131989
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171731
X-RAY DIFFRACTIONr_angle_refined_deg2.4011.6472717
X-RAY DIFFRACTIONr_angle_other_deg1.8461.5724038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.695268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.82622.35385
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.85915281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2671510
X-RAY DIFFRACTIONr_chiral_restr0.1760.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.022311
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02415
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_it1.6840.6641057
X-RAY DIFFRACTIONr_mcbond_other1.6840.6631056
X-RAY DIFFRACTIONr_mcangle_it1.7960.9951321
X-RAY DIFFRACTIONr_mcangle_other1.7960.9961322
X-RAY DIFFRACTIONr_scbond_it2.0030.827932
X-RAY DIFFRACTIONr_scbond_other2.0050.827932
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2121.1711394
X-RAY DIFFRACTIONr_long_range_B_refined2.7629.4312296
X-RAY DIFFRACTIONr_long_range_B_other2.5668.8252245
X-RAY DIFFRACTIONr_rigid_bond_restr7.25633720
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.57→1.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.151 110 -
Rwork0.054 2068 -
obs--95.57 %

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