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- PDB-5xg0: Crystal structure of a novel PET hydrolase from Ideonella sakaien... -

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Basic information

Entry
Database: PDB / ID: 5xg0
TitleCrystal structure of a novel PET hydrolase from Ideonella sakaiensis 201-F6
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / metal-binding / substrate binding / acidocalcisomal pyrophosphatase / inhibitor
Function / homology
Function and homology information


acetylesterase activity / poly(ethylene terephthalate) hydrolase / carboxylic ester hydrolase activity / xenobiotic catabolic process / extracellular region
Similarity search - Function
Dienelactone hydrolase family / Cutinase / PET hydrolase-like / : / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Poly(ethylene terephthalate) hydrolase
Similarity search - Component
Biological speciesIdeonella sakaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.58 Å
AuthorsHan, X. / Liu, W.D. / Zheng, Y.Y. / Chen, C.C. / Guo, R.T.
CitationJournal: Nat Commun / Year: 2017
Title: Structural insight into catalytic mechanism of PET hydrolase
Authors: Han, X. / Liu, W. / Huang, J.W. / Ma, J. / Zheng, Y. / Ko, T.P. / Xu, L. / Cheng, Y.S. / Chen, C.C. / Guo, R.T.
History
DepositionApr 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Dec 25, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: Poly(ethylene terephthalate) hydrolase


Theoretical massNumber of molelcules
Total (without water)83,6013
Polymers83,6013
Non-polymers00
Water20,2491124
1
A: Poly(ethylene terephthalate) hydrolase


Theoretical massNumber of molelcules
Total (without water)27,8671
Polymers27,8671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly(ethylene terephthalate) hydrolase


Theoretical massNumber of molelcules
Total (without water)27,8671
Polymers27,8671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Poly(ethylene terephthalate) hydrolase


Theoretical massNumber of molelcules
Total (without water)27,8671
Polymers27,8671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.480, 69.216, 153.041
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Poly(ethylene terephthalate) hydrolase / PETase


Mass: 27866.930 Da / Num. of mol.: 3 / Fragment: UNP residues 30-290
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ideonella sakaiensis (strain 201-F6) (bacteria)
Strain: 201-F6 / Gene: ISF6_4831 / Plasmid: pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1124 / 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: 2.01 Å3/Da / Density % sol: 38.83 % / Mosaicity: 0.29 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: Polyethylene Glycol 6000, Glycerol, MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 29, 2016
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→25 Å / Num. obs: 92787 / % possible obs: 99.8 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.018 / Rrim(I) all: 0.043 / Χ2: 1.54 / Net I/σ(I): 32.2 / Num. measured all: 499698
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.076 / Num. unique obs: 9169 / Rpim(I) all: 0.036 / Rrim(I) all: 0.084 / Χ2: 1.74 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
HKLdata reduction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WFI

4wfi


Resolution: 1.58→25 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.085 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.073
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1616 4552 4.9 %RANDOM
Rwork0.1372 ---
obs0.1384 88161 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 81.08 Å2 / Biso mean: 11.229 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--0.39 Å2-0 Å2
3----0.58 Å2
Refinement stepCycle: final / Resolution: 1.58→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5813 0 0 1124 6937
Biso mean---22.95 -
Num. residues----793
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195954
X-RAY DIFFRACTIONr_bond_other_d00.025237
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.9368113
X-RAY DIFFRACTIONr_angle_other_deg0.834312185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8465790
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81623.506231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.2715867
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2021539
X-RAY DIFFRACTIONr_chiral_restr0.1060.2889
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0216835
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021228
LS refinement shellResolution: 1.58→1.621 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.187 337 -
Rwork0.133 6285 -
all-6622 -
obs--97.37 %

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