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- PDB-7w1k: Crystal structure of carboxylesterase from Thermobifida fusca -

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Basic information

Entry
Database: PDB / ID: 7w1k
TitleCrystal structure of carboxylesterase from Thermobifida fusca
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
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 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


Theoretical massNumber of molelcules
Total (without water)52,9871
Polymers52,9871
Non-polymers00
Water13,151730
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18980 Å2
Unit cell
Length a, b, c (Å)45.277, 112.961, 54.780
Angle α, β, γ (deg.)90.000, 106.040, 90.000
Int Tables number4
Space group name H-MP1211

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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) / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P86325, carboxylesterase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 730 / Source method: isolated from a natural source / Formula: H2O

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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: 2.54 Å3/Da / Density % sol: 51.59 % / Mosaicity: 1.099 °
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, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 10, 2021
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.39→25 Å / Num. obs: 103778 / % possible obs: 99.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 13.79 Å2 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.026 / Rrim(I) all: 0.068 / Χ2: 0.722 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.456.50.563103650.8670.2350.6110.47999.5
1.45-1.516.40.406103550.9220.1720.4420.50199.4
1.51-1.5860.298102210.9460.130.3260.54698.2
1.58-1.666.60.227103590.9710.0940.2460.5899.6
1.66-1.766.80.171103830.9830.070.1850.62799.6
1.76-1.96.70.12104220.990.050.130.71299.6
1.9-2.096.50.083103040.9950.0340.090.81799
2.09-2.3970.063104600.9970.0250.0680.85299.8
2.39-3.016.60.049103880.9980.0210.0540.91999.4
3.01-2570.04105210.9980.0160.0441.11999.6

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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: 1.39→24.89 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 17.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1843 5188 5 %
Rwork0.1671 98559 -
obs0.168 103747 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.19 Å2 / Biso mean: 19.3672 Å2 / Biso min: 7.88 Å2
Refinement stepCycle: final / Resolution: 1.39→24.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3735 0 0 730 4465
Biso mean---30.21 -
Num. residues----496
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 (%)
1.39-1.440.24754940.22289390988494
1.44-1.50.22025190.201398581037799
1.5-1.570.21615160.185798051032198
1.57-1.650.20135200.1812988110401100
1.65-1.760.19155230.181992810451100
1.76-1.890.18125210.1725991310434100
1.89-2.080.18085180.170198371035599
2.08-2.380.18325270.16231000510532100
2.38-30.18755220.169199071042999
3-24.890.16645280.14931003510563100

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