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- PDB-9xug: Crystal structure of dsPETase05 in complex with terephthalic acid -

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Basic information

Entry
Database: PDB / ID: 9xug
TitleCrystal structure of dsPETase05 in complex with terephthalic acid
ComponentsAlpha/beta hydrolase
KeywordsHYDROLASE / PET hydrolase / PET degradation enzyme
Function / homologyCutinase / PET hydrolase-like / Alpha/Beta hydrolase fold / ACETATE ION / terephthalic acid / Alpha/beta hydrolase
Function and homology information
Biological speciesPseudomonadota bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLi, X. / Zhang, M.Z. / Huang, S.Q. / Zeng, C. / Huang, J.-W. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of dsPETase05 in complex with terephthalic acid
Authors: Li, X. / Zhang, M.Z. / Huang, S.Q. / Zeng, C. / Huang, J.-W. / Chen, C.-C. / Guo, R.-T.
History
DepositionNov 24, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2155
Polymers26,8711
Non-polymers3434
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-1 kcal/mol
Surface area9870 Å2
MethodPISA
2
A: Alpha/beta hydrolase
hetero molecules

A: Alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,42910
Polymers53,7432
Non-polymers6878
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_455-x-1/2,y,-z1
Buried area1860 Å2
ΔGint-7 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.473, 128.473, 128.473
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-767-

HOH

21A-810-

HOH

31A-831-

HOH

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Components

#1: Protein Alpha/beta hydrolase


Mass: 26871.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonadota bacterium (bacteria) / Gene: BXT89_15940 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1S8DDV9
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-UB7 / terephthalic acid / benzene-1,4-dicarboxylic acid


Mass: 166.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 3.29 Å3/Da / Density % sol: 62.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris propane pH 7.0, 3 M sodium acetate

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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: Sep 30, 2023
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: 56330 / % possible obs: 100 % / Redundancy: 9.3 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.03 / Rrim(I) all: 0.088 / Χ2: 0.915 / Net I/σ(I): 9.7 / Num. measured all: 522885
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.5-1.559.40.81755820.8550.960.2820.8650.462100
1.55-1.6210.30.56255750.9310.9820.1840.5920.496100
1.62-1.6910.20.40756210.960.990.1340.4290.533100
1.69-1.78100.2855850.9790.9950.0930.2950.595100
1.78-1.899.30.18456510.9890.9970.0640.1950.751100
1.89-2.049.40.1355640.9930.9980.0460.1381.041100
2.04-2.248.90.09756340.9950.9990.0350.1031.307100
2.24-2.569.20.07956580.9960.9990.0290.0841.498100
2.56-3.238.40.06156760.9980.9990.0230.0651.3899.9
3.23-257.80.04857840.99810.0180.0521.33699.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→23.47 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.673 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13704 2966 5.3 %RANDOM
Rwork0.10075 ---
obs0.10261 53364 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.617 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.5→23.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1890 0 24 331 2245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0132024
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171716
X-RAY DIFFRACTIONr_angle_refined_deg1.891.6452776
X-RAY DIFFRACTIONr_angle_other_deg1.6731.5714002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8055277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46222.62699
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.61415278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.8871510
X-RAY DIFFRACTIONr_chiral_restr0.1130.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022393
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02445
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_it2.3621.6391048
X-RAY DIFFRACTIONr_mcbond_other2.3271.6321044
X-RAY DIFFRACTIONr_mcangle_it2.6542.471310
X-RAY DIFFRACTIONr_mcangle_other2.6672.4751311
X-RAY DIFFRACTIONr_scbond_it3.6492.01976
X-RAY DIFFRACTIONr_scbond_other3.6532.013977
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5172.8941456
X-RAY DIFFRACTIONr_long_range_B_refined4.91422.3812383
X-RAY DIFFRACTIONr_long_range_B_other4.20621.0462298
X-RAY DIFFRACTIONr_rigid_bond_restr4.58333740
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.538 Å
RfactorNum. reflection% reflection
Rfree0.216 216 -
Rwork0.177 3909 -
obs--100 %

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