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- PDB-7w1j: Crystal structure of carboxylesterase from Thermobifida fusca with J1K -

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Basic information

Entry
Database: PDB / ID: 7w1j
TitleCrystal structure of carboxylesterase from Thermobifida fusca with J1K
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
4-(2-hydroxyethylcarbamoyl)benzoic acid / Carboxylesterase
Similarity search - Component
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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)53,1962
Polymers52,9871
Non-polymers2091
Water7,999444
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18720 Å2
Unit cell
Length a, b, c (Å)55.438, 79.943, 113.007
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Carboxylesterase


Mass: 52986.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P86325, carboxylesterase
#2: Chemical ChemComp-J1K / 4-(2-hydroxyethylcarbamoyl)benzoic acid


Mass: 209.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H11NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / 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: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% w/v Poly(acrylic acid sodium salt) 5100, 0.02 M MgCl2, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.92→30 Å / Num. obs: 38958 / % possible obs: 99.3 % / Redundancy: 13.2 % / CC1/2: 0.998 / Net I/σ(I): 15.1
Reflection shellResolution: 1.92→2.03 Å / Num. unique obs: 5964 / CC1/2: 0.825

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GOT

2got


Resolution: 1.92→30 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2191 3665 4.97 %
Rwork0.1803 70062 -
obs0.1822 38925 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.68 Å2 / Biso mean: 31.0692 Å2 / Biso min: 16.93 Å2
Refinement stepCycle: final / Resolution: 1.92→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3720 0 15 444 4179
Biso mean--41.75 36.93 -
Num. residues----494
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.92-1.990.32153510.2914675796
1.99-2.070.32073630.25477036100
2.07-2.160.27043730.22047066100
2.16-2.280.25463640.20487009100
2.28-2.420.253740.19587048100
2.42-2.610.24183700.18867001100
2.61-2.870.22893630.18227057100
2.87-3.280.22253730.18047028100
3.28-4.140.19333750.15427029100
4.14-300.16483590.15057031100

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