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- PDB-8h5l: Crystal structure of PETase N37D/S121E/R132E/A171C/A180V/P181V/D1... -

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Basic information

Entry
Database: PDB / ID: 8h5l
TitleCrystal structure of PETase N37D/S121E/R132E/A171C/A180V/P181V/D186H/S193C/A202C/V211C/S214Y/R224E/N233C/S242T/N246D/N275C/S282C/F284C mutant from Ideonella sakaiensis
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / PET hydrolase / Ideonella sakaiensis / mutant
Function / homology
Function and homology information


acetylesterase activity / poly(ethylene terephthalate) hydrolase / carboxylic ester hydrolase activity / xenobiotic catabolic process / extracellular region
Similarity search - Function
Cutinase / PET hydrolase-like / : / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
IODIDE ION / : / Poly(ethylene terephthalate) hydrolase
Similarity search - Component
Biological speciesIdeonella sakaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLee, S.H. / Seo, H. / Kim, K.-J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other government Korea, Republic Of
CitationJournal: To Be Published
Title: A case of balance engineering exhibits kinetic relationship between mesophilic and thermophilic poly(ethylene terephthalate) depolymerases.
Authors: Lee, S.H. / Seo, H. / Kim, K.J.
History
DepositionOct 13, 2022Deposition site: PDBJ / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 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
B: Poly(ethylene terephthalate) hydrolase
E: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,10214
Polymers94,9693
Non-polymers1,13311
Water18,7001038
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, size exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1645
Polymers31,6561
Non-polymers5084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8223
Polymers31,6561
Non-polymers1662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.168, 51.546, 100.370
Angle α, β, γ (deg.)90.00, 119.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Poly(ethylene terephthalate) hydrolase / PET hydrolase / PETase / PET-digesting enzyme


Mass: 31656.326 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ideonella sakaiensis (bacteria) / Gene: ISF6_4831 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1038 / 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: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / Details: 20 % PEG3350 and 0.2 M potassium iodide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 185509 / % possible obs: 95.8 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.971 / Χ2: 0.102 / Net I/σ(I): 7.3 / Num. measured all: 517120
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.7-1.732.70.64988481.51190.5
1.73-1.762.70.59588221.556191.6
1.76-1.792.70.53788581.563191.8
1.79-1.832.70.48589721.6192.6
1.83-1.872.80.42889881.669192.7
1.87-1.912.70.3790681.713193.4
1.91-1.962.80.31491001.839194.2
1.96-2.022.80.26492231.941195
2.02-2.072.80.2392672.058195.4
2.07-2.142.80.21492792.14196.2
2.14-2.222.80.18492982.242196.3
2.22-2.312.80.17294402.347197.2
2.31-2.412.80.1694332.489197.6
2.41-2.542.80.15195082.619198.1
2.54-2.72.90.1395752.816198.8
2.7-2.912.90.12296093.01199.1
2.91-3.22.90.10695943.353199.2
3.2-3.662.90.08995783.828199.1
3.66-4.612.70.07895964.195198.8
4.61-502.70.0894534.144197.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000data reduction
PDB_EXTRACT3.27data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XJH

5xjh


Resolution: 1.7→27.97 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.853 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18475 4474 4.6 %RANDOM
Rwork0.15458 ---
obs0.15595 91891 96.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.236 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20.46 Å2
2---0.94 Å20 Å2
3---0.1 Å2
Refinement stepCycle: 1 / Resolution: 1.7→27.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5762 0 11 1038 6811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0126136
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165244
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.6418396
X-RAY DIFFRACTIONr_angle_other_deg0.5781.55212312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9025835
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.979536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71110915
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0870.2917
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027305
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021227
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_it1.3191.3553271
X-RAY DIFFRACTIONr_mcbond_other1.3151.3553271
X-RAY DIFFRACTIONr_mcangle_it1.9292.0244129
X-RAY DIFFRACTIONr_mcangle_other1.9292.0254130
X-RAY DIFFRACTIONr_scbond_it2.0011.5242865
X-RAY DIFFRACTIONr_scbond_other2.0011.5252866
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8972.2154268
X-RAY DIFFRACTIONr_long_range_B_refined5.61329.0527402
X-RAY DIFFRACTIONr_long_range_B_other4.71922.1527019
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.741 Å
RfactorNum. reflection% reflection
Rfree0.249 354 -
Rwork0.224 6158 -
obs--89.43 %

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