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- PDB-5xh2: Crystal structure of a novel PET hydrolase R103G/S131A mutant in ... -

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Basic information

Entry
Database: PDB / ID: 5xh2
TitleCrystal structure of a novel PET hydrolase R103G/S131A mutant in complex with pNP from Ideonella sakaiensis 201-F6
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, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
P-NITROPHENOL / Poly(ethylene terephthalate) hydrolase
Similarity search - Component
Biological speciesIdeonella sakaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 19, 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 1.2Nov 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 1.3Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8906
Polymers27,3661
Non-polymers5235
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-13 kcal/mol
Surface area9720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.784, 51.532, 84.373
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: 27366.400 Da / Num. of mol.: 1 / Mutation: R103G,S131A
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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NPO / P-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.02 Å3/Da / Density % sol: 39.02 % / Mosaicity: 0.163 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Ammonium Sulfate, NaCl, HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 16, 2017
RadiationMonochromator: LN2 cooled Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.2→25 Å / Num. obs: 69716 / % possible obs: 99.8 % / Redundancy: 8 % / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.019 / Rrim(I) all: 0.053 / Χ2: 0.649 / Net I/σ(I): 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.2-1.247.60.2120.9820.0810.2280.4498.9
1.24-1.297.90.1770.9880.0660.1890.45699.6
1.29-1.3580.150.9910.0560.160.49199.5
1.35-1.4280.1290.9920.0480.1380.5699.8
1.42-1.5180.1040.9950.0390.1110.66599.9
1.51-1.638.10.080.9960.030.0850.713100
1.63-1.798.10.0640.9980.0240.0680.802100
1.79-2.058.10.050.9980.0190.0540.805100
2.05-2.5880.0390.9990.0150.0420.797100
2.58-257.80.0360.9990.0140.0380.72199.9

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Processing

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

4wfi


Resolution: 1.2→25 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.773 / SU ML: 0.016 / SU R Cruickshank DPI: 0.0273 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.029
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1246 3391 4.9 %RANDOM
Rwork0.0984 ---
obs0.0997 66256 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 108.74 Å2 / Biso mean: 10.757 Å2 / Biso min: 4.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-0 Å20 Å2
2--0.29 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1912 0 30 365 2307
Biso mean--25.36 27.26 -
Num. residues----261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022028
X-RAY DIFFRACTIONr_bond_other_d00.021766
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.952782
X-RAY DIFFRACTIONr_angle_other_deg0.8213.0014127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5965280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.72923.68476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.44115295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1511512
X-RAY DIFFRACTIONr_chiral_restr0.1060.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212328
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02416
X-RAY DIFFRACTIONr_rigid_bond_restr7.10333794
X-RAY DIFFRACTIONr_sphericity_free26.5255224
X-RAY DIFFRACTIONr_sphericity_bonded9.79353882
LS refinement shellResolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.14 223 -
Rwork0.103 4705 -
all-4928 -
obs--96.99 %

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