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- PDB-7w1i: Crystal structure of carboxylesterase mutant from Thermobifida fu... -

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Basic information

Entry
Database: PDB / ID: 7w1i
TitleCrystal structure of carboxylesterase mutant from Thermobifida fusca with C8X and C9C
ComponentsCarboxylesterase
KeywordsHYDROLASE / plastic degradation / catalysis
Function / homology
Function and homology information


carboxylesterase / carboxylesterase activity / extracellular region
Similarity search - Function
: / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
bis(2-hydroxyethyl) benzene-1,4-dicarboxylate / 4-(2-hydroxyethyloxycarbonyl)benzoic acid / Carboxylesterase
Similarity search - Component
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsHan, X. / Gerlis, H. / Li, Z. / Gao, J. / Wei, R. / Liu, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Catalysis / Year: 2022
Title: Structural Insights into (Tere)phthalate-Ester Hydrolysis by a Carboxylesterase and Its Role in Promoting PET Depolymerization
Authors: Von Haugwitz, G. / Han, X. / Pfaff, L. / Li, Q. / Wei, H. / Gao, J. / Methling, K. / Ao, Y. / Brack, Y. / Mican, J. / Feiler, C.G. / Weiss, M.S. / Bednar, D. / Palm, G.J. / Lalk, M. / ...Authors: Von Haugwitz, G. / Han, X. / Pfaff, L. / Li, Q. / Wei, H. / Gao, J. / Methling, K. / Ao, Y. / Brack, Y. / Mican, J. / Feiler, C.G. / Weiss, M.S. / Bednar, D. / Palm, G.J. / Lalk, M. / Lammers, M. / Damborsky, J. / Weber, G. / Liu, W. / Bornscheuer, U.T. / Wei, R.
History
DepositionNov 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: 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.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4353
Polymers52,9711
Non-polymers4642
Water12,412689
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17770 Å2
Unit cell
Length a, b, c (Å)44.744, 110.236, 53.418
Angle α, β, γ (deg.)90.000, 106.420, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carboxylesterase


Mass: 52970.543 Da / Num. of mol.: 1 / Mutation: E319L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (bacteria) / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / References: UniProt: P86325, carboxylesterase
#2: Chemical ChemComp-C8X / bis(2-hydroxyethyl) benzene-1,4-dicarboxylate / bis(2-hydroxyethyl) terephthalate


Mass: 254.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-C9C / 4-(2-hydroxyethyloxycarbonyl)benzoic acid / monohydroxyethyl terephthalate


Mass: 210.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 689 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.39 Å3/Da / Density % sol: 48.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25 % Poly (acrylic acid sodium salt) 5100, 0.02 M MgCl2, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.67→25 Å / Num. obs: 56837 / % possible obs: 98.7 % / Redundancy: 7.4 % / CC1/2: 0.994 / Net I/σ(I): 17
Reflection shellResolution: 1.67→1.73 Å / Num. unique obs: 5459 / CC1/2: 0.84

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OGS

2ogs


Resolution: 1.67→24.27 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.208 2832 5.01 %
Rwork0.1797 53726 -
obs0.1811 56558 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.52 Å2 / Biso mean: 17.1134 Å2 / Biso min: 5.33 Å2
Refinement stepCycle: final / Resolution: 1.67→24.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3743 0 33 689 4465
Biso mean--26.54 26.3 -
Num. residues----497
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.67-1.730.27292720.22125161543395
1.73-1.80.24612810.19815358563998
1.8-1.880.31542830.27215353563699
1.88-1.980.21862850.19465399568499
1.98-2.10.18322790.1645312559198
2.1-2.270.2662840.23785351563598
2.27-2.490.22642870.171454565743100
2.49-2.850.20932850.164554185703100
2.85-3.590.17832880.158454655753100
3.59-24.270.16182880.15235453574199

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