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- PDB-6qgc: PETase from Ideonella sakaiensis without ligand -

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Basic information

Entry
Database: PDB / ID: 6qgc
TitlePETase from Ideonella sakaiensis without ligand
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / PET degradation
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
Poly(ethylene terephthalate) hydrolase
Similarity search - Component
Biological speciesIdeonella sakaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPalm, G.J. / Reisky, L. / Boettcher, D. / Mueller, H. / Michels, E.A.P. / Walczak, C. / Berndt, L. / Weiss, M.S. / Bornscheuer, U.T. / Weber, G.
CitationJournal: Nat Commun / Year: 2019
Title: Structure of the plastic-degrading Ideonella sakaiensis MHETase bound to a substrate.
Authors: Palm, G.J. / Reisky, L. / Bottcher, D. / Muller, H. / Michels, E.A.P. / Walczak, M.C. / Berndt, L. / Weiss, M.S. / Bornscheuer, U.T. / Weber, G.
History
DepositionJan 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Poly(ethylene terephthalate) hydrolase
B: Poly(ethylene terephthalate) hydrolase
C: Poly(ethylene terephthalate) hydrolase
D: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,51311
Polymers121,0834
Non-polymers4307
Water8,179454
1
A: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4023
Polymers30,2711
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3062
Polymers30,2711
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4984
Polymers30,2711
Non-polymers2283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3062
Polymers30,2711
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.121, 78.769, 140.121
Angle α, β, γ (deg.)90.00, 92.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 30270.783 Da / Num. of mol.: 4
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.33 Å3/Da / Density % sol: 47.16 % / Description: plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1 ul protein (10 mg/ml, 20 mM TRIS pH 7.5, 150 mM NaCl) + 1 ul reservoir (0.1 M sodium citrate or sodium acetate pH 5.0, 15% (v/v) PEG8000, 0.5 M lithium sulfate)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9799 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2017 / Details: mirror
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9799 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 73090 / % possible obs: 97.1 % / Redundancy: 4.2 % / Biso Wilson estimate: 27.1 Å2 / CC1/2: 0.991 / Rrim(I) all: 0.151 / Rsym value: 0.131 / Net I/σ(I): 8.4
Reflection shellResolution: 2→2.12 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 11574 / CC1/2: 0.62 / Rrim(I) all: 0.838 / Rsym value: 0.719 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSJun 1, 2017data reduction
XDSJun 1, 2017data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CG1

4cg1


Resolution: 2→48.73 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.9 / SU B: 12.568 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.183 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26091 3607 4.9 %RANDOM
Rwork0.21347 ---
obs0.21578 69684 97.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.386 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å2-0 Å20.33 Å2
2---2.11 Å20 Å2
3---0.78 Å2
Refinement stepCycle: 1 / Resolution: 2→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7689 0 19 454 8162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0147902
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176728
X-RAY DIFFRACTIONr_angle_refined_deg1.8171.65610780
X-RAY DIFFRACTIONr_angle_other_deg1.0521.63415832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.40651048
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.80221.556360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.874151148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4021552
X-RAY DIFFRACTIONr_chiral_restr0.0860.21085
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029151
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021473
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_it0.3850.814186
X-RAY DIFFRACTIONr_mcbond_other0.3850.814185
X-RAY DIFFRACTIONr_mcangle_it0.6581.2135227
X-RAY DIFFRACTIONr_mcangle_other0.6581.2135228
X-RAY DIFFRACTIONr_scbond_it0.5870.8843716
X-RAY DIFFRACTIONr_scbond_other0.5170.8723703
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8261.2875532
X-RAY DIFFRACTIONr_long_range_B_refined4.46710.3118831
X-RAY DIFFRACTIONr_long_range_B_other4.40110.0618766
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 262 -
Rwork0.303 4823 -
obs--91.11 %
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)
11.0663-0.2222-0.14870.6538-0.07750.4528-0.00190.0574-0.0479-0.02910.00730.0502-0.00030.0275-0.00540.0067-0.0057-0.03730.2332-0.00710.251810.355-14.618194.083
20.6480.18-0.21040.6553-0.21320.52540.0227-0.0691-0.02590.073-0.00540.0264-0.02870.0303-0.01730.0129-0.004-0.03150.2326-0.00560.261835.697-12.424222.624
31.0816-0.3261-0.06780.80370.0640.48280.03430.06020.0458-0.0509-0.0059-0.0301-0.0398-0.0364-0.02840.01270.0054-0.0370.2203-0.0010.257418.883-29.573264.311
40.6043-0.09730.20660.5982-0.13740.48210.01110.0584-0.0148-0.0695-0.01630.02120.02590.03310.00520.01640.004-0.04730.2291-0.00190.254632.5647.468267.145
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 290
2X-RAY DIFFRACTION2B29 - 289
3X-RAY DIFFRACTION3C28 - 289
4X-RAY DIFFRACTION4D29 - 289

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