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- PDB-8b4u: The crystal structure of PET46, a PETase enzyme from Candidatus b... -

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Basic information

Entry
Database: PDB / ID: 8b4u
TitleThe crystal structure of PET46, a PETase enzyme from Candidatus bathyarchaeota
ComponentsAlpha/beta hydrolase
KeywordsHYDROLASE / PETase / PET / enzyme / esterase / plastic / degradation / biotech / enzyme evolution
Function / homologyPeptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / serine-type peptidase activity / Alpha/Beta hydrolase fold / proteolysis / PHOSPHATE ION / Alpha/beta hydrolase
Function and homology information
Biological speciesCandidatus Bathyarchaeota archaeon (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsCostanzi, E. / Applegate, V. / Schumacher, J. / Smits, S.H.J.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)417919780 Germany
German Federal Ministry for Education and Research31B0837A Germany
CitationJournal: Commun Chem / Year: 2023
Title: An archaeal lid-containing feruloyl esterase degrades polyethylene terephthalate.
Authors: Perez-Garcia, P. / Chow, J. / Costanzi, E. / Gurschke, M. / Dittrich, J. / Dierkes, R.F. / Molitor, R. / Applegate, V. / Feuerriegel, G. / Tete, P. / Danso, D. / Thies, S. / Schumacher, J. / ...Authors: Perez-Garcia, P. / Chow, J. / Costanzi, E. / Gurschke, M. / Dittrich, J. / Dierkes, R.F. / Molitor, R. / Applegate, V. / Feuerriegel, G. / Tete, P. / Danso, D. / Thies, S. / Schumacher, J. / Pfleger, C. / Jaeger, K.E. / Gohlke, H. / Smits, S.H.J. / Schmitz, R.A. / Streit, W.R.
History
DepositionSep 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Database references / Category: citation / citation_author
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.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,86526
Polymers31,2091
Non-polymers1,65725
Water3,495194
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint21 kcal/mol
Surface area12390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.292, 79.292, 171.546
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Alpha/beta hydrolase


Mass: 31208.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Bathyarchaeota archaeon (archaea)
Gene: DRO64_06360 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A497NK85
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.49 Å3/Da / Density % sol: 50.68 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / Details: 325 mM (NH4)H2PO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.71→68.67 Å / Num. obs: 34960 / % possible obs: 99.4 % / Redundancy: 8.5 % / Biso Wilson estimate: 29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.7
Reflection shellResolution: 1.71→1.74 Å / Num. unique obs: 1831 / CC1/2: 0.559

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: alphafold model

Resolution: 1.71→36.38 Å / SU ML: 0.1874 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.4104
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1727 1725 4.94 %
Rwork0.1523 33228 -
obs0.1534 34953 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.79 Å2
Refinement stepCycle: LAST / Resolution: 1.71→36.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2119 0 101 194 2414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01062308
X-RAY DIFFRACTIONf_angle_d1.01313087
X-RAY DIFFRACTIONf_chiral_restr0.067338
X-RAY DIFFRACTIONf_plane_restr0.0114398
X-RAY DIFFRACTIONf_dihedral_angle_d13.3472860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.760.32761430.28632752X-RAY DIFFRACTION99.86
1.76-1.820.23141330.22822723X-RAY DIFFRACTION99.76
1.82-1.880.26361380.1942744X-RAY DIFFRACTION99.69
1.88-1.960.20521390.17362721X-RAY DIFFRACTION99.83
1.96-2.050.20131410.17932744X-RAY DIFFRACTION99.59
2.05-2.150.19581320.14772752X-RAY DIFFRACTION99.48
2.15-2.290.15371350.13882765X-RAY DIFFRACTION99.35
2.29-2.470.13811390.1312772X-RAY DIFFRACTION99.25
2.47-2.710.16441540.14072751X-RAY DIFFRACTION98.78
2.71-3.110.16611700.13432747X-RAY DIFFRACTION98.61
3.11-3.910.14651640.13182800X-RAY DIFFRACTION97.95
3.91-36.380.18171370.16482957X-RAY DIFFRACTION95.94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.61612433356-1.44174815019-0.04377285234622.031306185040.1636888897394.414000751240.09753439000310.06807440547030.0818393690636-0.0665827667657-0.04985366611160.092707771462-0.0425736019154-0.332214502947-0.03237780277850.1928898686530.0105353808657-0.005392852526740.2243687593730.02459626748330.196137388798-16.525543769172.59849279085.89657214686
21.309150480810.166749523617-0.293542290772.20796937683-0.01456815869122.446479993390.01439339880510.0143967504759-0.03988092920620.04962431841070.03459110356410.1689092315140.0833539381845-0.131855496422-0.05995995049680.2285626739680.00381337472878-0.01589974463220.1837392213830.007698252079010.192396626277-10.866668245968.82803588810.7573070552
34.968500223031.387885760510.6976528653562.11499828870.5567081821061.91908986410.0390671882125-0.3577731586430.04306433842060.297310951274-0.05116740178710.2258581530250.0251417197479-0.2078427150130.01306072521660.3024691792880.02730292203970.02903262969060.1908540371420.03047528583430.235959042965-12.428598887871.025849496620.8667465591
42.740915715763.7779504947-1.885270459587.95021961322-4.551827907853.6439141512-0.0129457565636-0.0867518299402-0.1118081449050.0160878836829-0.31348967356-0.610967453708-0.1423210339590.4853164110040.3705870595040.267899036307-0.0109164782907-0.02450832702370.2525227701640.001912866312530.2476505109798.5089437935281.9386101812.6615208394
50.4119465797180.679994185157-0.377217664391.82616150987-1.424970646482.342392065050.0362263641812-0.002658834809160.08322121665580.2213481982650.0247082437429-0.00380975713553-0.258821358910.137707144381-0.09486509083650.2720774692470.0116145818898-0.02824484215280.220207660185-0.01506950526310.2738446360692.6178914807580.520800065414.9893407914
63.002316621-0.128326852688-1.955799287951.909219442120.3515511107186.82095042931-0.0307361193838-0.0820533888389-0.0948282861030.3278528303840.0885336917635-0.1995359645080.1702110241330.383068546987-0.02804611406550.2622909882850.061116427615-0.07011611674220.2117496776580.00525248900850.2679175831666.6478605170464.704444980522.6877256716
73.22559916213-0.644616798155-0.6602455250882.63768426160.639651888384.79983978482-0.0928753129045-0.0682514622932-0.5531338079910.4748800969770.02039659642120.4015229553940.848004692792-0.4745729303360.2084366107920.498921341611-0.02978083371640.0070221537590.2543846568490.03082439939480.384356665786-6.7468673989254.340714702920.7097458713
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 19 )1 - 191 - 19
22chain 'A' and (resid 20 through 100 )20 - 10020 - 100
33chain 'A' and (resid 101 through 132 )101 - 132101 - 132
44chain 'A' and (resid 133 through 161 )133 - 161133 - 161
55chain 'A' and (resid 162 through 203 )162 - 203162 - 203
66chain 'A' and (resid 204 through 242 )204 - 242204 - 242
77chain 'A' and (resid 243 through 269 )243 - 269243 - 269

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