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- PDB-9kl9: crystal structure of a mutant Poly(Ethylene terephthalate) hydrolase -

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Basic information

Entry
Database: PDB / ID: 9kl9
Titlecrystal structure of a mutant Poly(Ethylene terephthalate) hydrolase
ComponentsPoly(Ethylene terephthalate) hydrolase
KeywordsHYDROLASE / mutant / dimer
Function / homologyAlpha/beta hydrolase fold-5 / Alpha/beta hydrolase family / poly(ethylene terephthalate) hydrolase / Alpha/Beta hydrolase fold / hydrolase activity / Poly(Ethylene terephthalate) hydrolase
Function and homology information
Biological speciesbacterium HR29 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWang, H. / Feng, Y. / Du, X.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Commun Biol / Year: 2025
Title: Computational loop reconstruction based design of efficient PET hydrolases.
Authors: Wang, H. / Cun, Y. / Wang, M. / Du, X. / Yang, Z. / Wang, H. / Zhang, J. / Wang, P. / Feng, Y. / Zhu, Y.
History
DepositionNov 14, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 1, 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
B: Poly(Ethylene terephthalate) hydrolase


Theoretical massNumber of molelcules
Total (without water)58,6362
Polymers58,6362
Non-polymers00
Water00
1
A: Poly(Ethylene terephthalate) hydrolase


Theoretical massNumber of molelcules
Total (without water)29,3181
Polymers29,3181
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly(Ethylene terephthalate) hydrolase


Theoretical massNumber of molelcules
Total (without water)29,3181
Polymers29,3181
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.713, 51.615, 56.679
Angle α, β, γ (deg.)103.233, 103.613, 96.661
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Poly(Ethylene terephthalate) hydrolase


Mass: 29317.771 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) bacterium HR29 (bacteria) / Gene: HRbin29_00073 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A2H5Z9R5, poly(ethylene terephthalate) hydrolase
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: 39.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.5 M NaCl, 100 mM imidazole pH8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.899→32.17 Å / Num. obs: 10117 / % possible obs: 97.23 % / Redundancy: 3.5 % / Biso Wilson estimate: 24.45 Å2 / CC1/2: 0.805 / Net I/σ(I): 6.19
Reflection shellResolution: 2.9→3.19 Å / Num. unique obs: 2511 / CC1/2: 0.336

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
xia2data reduction
xia2data scaling
PHENIXphasing
Cootmodel building
PHENIX1.21.1_5286refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→32.17 Å / SU ML: 0.3509 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.5519
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2353 498 5.01 %
Rwork0.1945 9444 -
obs0.1966 9942 97.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.63 Å2
Refinement stepCycle: LAST / Resolution: 2.9→32.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3916 0 0 0 3916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00324016
X-RAY DIFFRACTIONf_angle_d0.62045503
X-RAY DIFFRACTIONf_chiral_restr0.0454630
X-RAY DIFFRACTIONf_plane_restr0.0066721
X-RAY DIFFRACTIONf_dihedral_angle_d12.79871431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.190.31940.24762287X-RAY DIFFRACTION93.26
3.19-3.650.28241300.21772361X-RAY DIFFRACTION97.42
3.65-4.60.221380.16662387X-RAY DIFFRACTION98.75
4.6-32.170.18351360.17392409X-RAY DIFFRACTION99.57

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