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- PDB-8cru: PETase Ancestral Sequence Reconstruction 008 -

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Basic information

Entry
Database: PDB / ID: 8cru
TitlePETase Ancestral Sequence Reconstruction 008
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / PETase / ancestral sequence reconstruction
Function / homologyCITRIC ACID
Function and homology information
Biological speciesIdeonella sakaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsJoho, Y. / Royan, S. / Caputo, A.T. / Ardevol Grau, A. / Jackson, C.
Funding support Australia, 1items
OrganizationGrant numberCountry
Other government Australia
CitationJournal: Biochemistry / Year: 2023
Title: Ancestral Sequence Reconstruction Identifies Structural Changes Underlying the Evolution of Ideonella sakaiensis PETase and Variants with Improved Stability and Activity.
Authors: Joho, Y. / Vongsouthi, V. / Spence, M.A. / Ton, J. / Gomez, C. / Tan, L.L. / Kaczmarski, J.A. / Caputo, A.T. / Royan, S. / Jackson, C.J. / Ardevol, A.
History
DepositionMay 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 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)29,1022
Polymers28,9101
Non-polymers1921
Water7,206400
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.013, 86.013, 88.924
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-764-

HOH

21A-796-

HOH

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Components

#1: Protein Poly(ethylene terephthalate) hydrolase


Mass: 28909.955 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ideonella sakaiensis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: poly(ethylene terephthalate) hydrolase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 3.28 Å3/Da / Density % sol: 62.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3 / Details: 1.2 M Trisodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.3→44.46 Å / Num. obs: 93527 / % possible obs: 99.8 % / Redundancy: 20.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.032 / Rrim(I) all: 0.145 / Net I/σ(I): 11.7 / Num. measured all: 1900259 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.3-1.3219.21.7638419843830.7470.4041.811.495.6
7.12-44.4617.30.043114286600.9990.010.04448.599.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0350refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XJH

5xjh


Resolution: 1.3→43.044 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.982 / WRfactor Rfree: 0.124 / WRfactor Rwork: 0.104 / SU B: 1.141 / SU ML: 0.02 / Average fsc free: 0.9847 / Average fsc work: 0.9883 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.029
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1331 4683 5.01 %RANDOM
Rwork0.1108 88786 --
all0.112 ---
obs-93469 99.894 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 12.379 Å2
Baniso -1Baniso -2Baniso -3
1-0.049 Å20.024 Å20 Å2
2--0.049 Å2-0 Å2
3----0.159 Å2
Refinement stepCycle: LAST / Resolution: 1.3→43.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1955 0 13 400 2368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122111
X-RAY DIFFRACTIONr_bond_other_d0.0250.0161821
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.6332902
X-RAY DIFFRACTIONr_angle_other_deg0.8251.5454306
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1595301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.7741012
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.68410322
X-RAY DIFFRACTIONr_dihedral_angle_6_deg18.931079
X-RAY DIFFRACTIONr_chiral_restr0.1050.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022500
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02416
X-RAY DIFFRACTIONr_nbd_refined0.2260.2394
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.21615
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21063
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21048
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2294
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1450.213
X-RAY DIFFRACTIONr_nbd_other0.1490.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2180.255
X-RAY DIFFRACTIONr_mcbond_it1.9761.1651102
X-RAY DIFFRACTIONr_mcbond_other1.9421.1651102
X-RAY DIFFRACTIONr_mcangle_it2.0961.7631389
X-RAY DIFFRACTIONr_mcangle_other2.1031.7671390
X-RAY DIFFRACTIONr_scbond_it2.8241.3681009
X-RAY DIFFRACTIONr_scbond_other2.8231.3651006
X-RAY DIFFRACTIONr_scangle_it3.0211.9681497
X-RAY DIFFRACTIONr_scangle_other3.021.9691498
X-RAY DIFFRACTIONr_lrange_it4.58128.3532600
X-RAY DIFFRACTIONr_lrange_other3.22718.7612427
X-RAY DIFFRACTIONr_rigid_bond_restr7.77333932
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.3-1.3340.2573600.21364010.21668430.9610.96898.80170.211
1.334-1.370.2053280.19563050.19666330.9740.9741000.193
1.37-1.410.1983090.18162210.18265300.9740.9781000.177
1.41-1.4530.182650.15760570.15863220.9790.9841000.149
1.453-1.5010.1693390.13457390.13660780.9820.9881000.123
1.501-1.5540.1522970.12556390.12659360.9850.991000.112
1.554-1.6120.1382870.11154520.11357390.9880.9921000.098
1.612-1.6780.1332700.10452520.10555220.9890.9931000.091
1.678-1.7520.1292770.09250430.09453200.9910.9951000.08
1.752-1.8380.1133140.08747260.08950400.9920.9951000.076
1.838-1.9370.1182430.08746060.08948490.9910.9961000.077
1.937-2.0540.0922120.08543610.08545730.9940.9961000.077
2.054-2.1960.1061890.08341220.08443110.9930.9961000.075
2.196-2.3710.12050.08438160.08540210.9940.9961000.078
2.371-2.5970.1281980.09435120.09637100.9910.9951000.088
2.597-2.9020.1381640.1132130.11233770.9890.9931000.107
2.902-3.3480.1271290.10728710.10830000.9910.9931000.108
3.348-4.0950.1091230.08824150.08925380.9930.9951000.093
4.095-5.7650.1241260.1118980.11120240.9930.9941000.119
5.765-43.0440.178480.19311370.19311860.9780.97899.91570.211

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