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- PDB-7cy0: Crystal structure of S185H mutant PET hydrolase from Ideonella sa... -

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Basic information

Entry
Database: PDB / ID: 7cy0
TitleCrystal structure of S185H mutant PET hydrolase from Ideonella sakaiensis
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / Poly(ethylene terephthalate) hydrolase / substrate binding / 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
Similarity search - Domain/homology
ACETIC ACID / Poly(ethylene terephthalate) hydrolase
Similarity search - Component
Biological speciesIdeonella sakaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsHan, X. / Liu, W.D. / Zheng, Y.Y. / Chen, C.C. / Guo, R.T.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)3180062 China
Chinese Academy of SciencesKFJ-STS-ZDTP-064 China
CitationJournal: Nat Catal / Year: 2021
Title: General features to enhance enzymatic activity of poly(ethylene terephthalate) hydrolysis.
Authors: Che, C.C. / Han, X. / Li, X. / Jiang, P. / Niu, D. / Ma, L. / Liu, W. / Li, S. / Qu, Y. / Hu, H. / Min, J. / Yang, Y. / Zhang, L. / Zeng, W. / Huang, J.W. / Dai, L. / Guo, R.T.
History
DepositionSep 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _struct.title
Revision 1.2Nov 29, 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 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)27,4664
Polymers27,2861
Non-polymers1803
Water5,945330
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9450 Å2
Unit cell
Length a, b, c (Å)50.925, 51.806, 84.287
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 / PET-digesting enzyme


Mass: 27286.275 Da / Num. of mol.: 1 / Mutation: R103G, S131A, S214H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ideonella sakaiensis (strain NBRC 110686 / TISTR 2288 / 201-F6) (bacteria)
Strain: NBRC 110686 / TISTR 2288 / 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: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.04 Å3/Da / Density % sol: 39.63 % / Mosaicity: 1.097 °
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 29, 2019
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.32→25 Å / Num. obs: 51200 / % possible obs: 96.7 % / Redundancy: 7 % / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.018 / Rrim(I) all: 0.049 / Χ2: 1.528 / Net I/σ(I): 14 / Num. measured all: 360092
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.32-1.3770.43849700.9330.1760.4731.3695.5
1.37-1.4270.33450170.9590.1350.3611.42795.8
1.42-1.4970.24349930.9780.0980.2631.46396
1.49-1.5670.17550360.9870.0710.191.46196
1.56-1.666.90.13550180.9910.0540.1461.57995.9
1.66-1.796.90.09650170.9960.0390.1041.61595.3
1.79-1.9770.06250840.9980.0250.0671.36296.4
1.97-2.267.20.05152430.9980.0210.0551.78198.7
2.26-2.847.40.03953090.9990.0150.0421.6599
2.84-2570.02855130.9990.0110.0311.54398.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XG0

5xg0


Resolution: 1.32→24.71 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.685 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1656 2481 4.9 %RANDOM
Rwork0.144 ---
obs0.1451 48671 96.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.25 Å2 / Biso mean: 13.769 Å2 / Biso min: 8.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å2-0 Å20 Å2
2---0.61 Å20 Å2
3---1.13 Å2
Refinement stepCycle: final / Resolution: 1.32→24.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1915 0 12 330 2257
Biso mean--20.21 28.36 -
Num. residues----261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131984
X-RAY DIFFRACTIONr_bond_other_d00.0171792
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.6412707
X-RAY DIFFRACTIONr_angle_other_deg1.5391.5724129
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8285266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.49521.79889
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.3915285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8461512
X-RAY DIFFRACTIONr_chiral_restr0.0860.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.022359
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02473
LS refinement shellResolution: 1.322→1.356 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 208 -
Rwork0.216 3409 -
all-3617 -
obs--94.09 %

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