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- PDB-7w1l: Crystal structure of carboxylesterase mutant from Thermobifida fu... -

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Basic information

Entry
Database: PDB / ID: 7w1l
TitleCrystal structure of carboxylesterase mutant from Thermobifida fusca with C8X
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 / Carboxylesterase
Similarity search - Component
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 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)53,2252
Polymers52,9711
Non-polymers2541
Water3,783210
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18010 Å2
Unit cell
Length a, b, c (Å)44.542, 109.934, 53.214
Angle α, β, γ (deg.)90.000, 106.270, 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: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.35 Å3/Da / Density % sol: 47.59 % / Mosaicity: 1.559 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1.0 M sodium citrate, 0.1 M Imidazole pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2019
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.43→25 Å / Num. obs: 18029 / % possible obs: 99.7 % / Redundancy: 7.2 % / Biso Wilson estimate: 26.05 Å2 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.072 / Rrim(I) all: 0.195 / Χ2: 0.885 / Net I/σ(I): 4 / Num. measured all: 130648
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.43-2.527.10.55817870.8910.2220.6010.56299.9
2.52-2.627.50.54717920.8550.2110.5870.821100
2.62-2.747.50.40117880.9440.1540.430.62599.9
2.74-2.887.50.33118190.9590.1290.3560.64599.8
2.88-3.067.40.25717950.9670.10.2760.73999.9
3.06-3.37.20.20618100.9810.0820.2220.94699.7
3.3-3.636.40.18317760.9770.0780.21.42598.9
3.63-4.157.60.13918100.9830.0540.1491.12299.9
4.15-5.227.50.09818150.9920.0390.1060.95599.8
5.22-256.80.09218370.9930.0380.11.09499.4

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Processing

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

2ogt


Resolution: 2.44→25 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2225 901 5.01 %
Rwork0.1623 17093 -
obs0.1653 17994 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.06 Å2 / Biso mean: 28.1606 Å2 / Biso min: 11.62 Å2
Refinement stepCycle: final / Resolution: 2.44→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3743 0 18 210 3971
Biso mean--36.59 29.19 -
Num. residues----497
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.44-2.590.25961380.2078261491
2.59-2.790.27861540.18842918100
2.79-3.070.26531500.18722861100
3.07-3.520.20911520.1668287599
3.52-4.420.2131520.14072918100
4.43-250.18171550.1422290799

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