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- PDB-7xri: Feruloyl esterase mutant -S106A -

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Basic information

Entry
Database: PDB / ID: 7xri
TitleFeruloyl esterase mutant -S106A
ComponentsCinnamoyl esterase
KeywordsHYDROLASE / Feruloyl esterase mutant (S101A) complexed with ethyl ferulate
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / carboxylic ester hydrolase activity
Similarity search - Function
: / Serine aminopeptidase, S33 / Dienelactone hydrolase / Dienelactone hydrolase family / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Chem-ZYC / Cinnamoyl esterase
Similarity search - Component
Biological speciesLactobacillus acidophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsHwang, J.S. / Lee, J.H. / Do, H. / Lee, C.W.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)PM22030 Korea, Republic Of
CitationJournal: Int J Mol Sci / Year: 2023
Title: Feruloyl Esterase ( La Fae) from Lactobacillus acidophilus : Structural Insights and Functional Characterization for Application in Ferulic Acid Production.
Authors: Jeon, S. / Hwang, J. / Do, H. / Le, L.T.H.L. / Lee, C.W. / Yoo, W. / Lee, M.J. / Shin, S.C. / Kim, K.K. / Kim, H.W. / Lee, J.H.
History
DepositionMay 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / pdbx_database_related
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cinnamoyl esterase
B: Cinnamoyl esterase
C: Cinnamoyl esterase
D: Cinnamoyl esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,2218
Polymers114,3334
Non-polymers8894
Water7,927440
1
A: Cinnamoyl esterase
B: Cinnamoyl esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6114
Polymers57,1662
Non-polymers4442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-7 kcal/mol
Surface area20650 Å2
MethodPISA
2
C: Cinnamoyl esterase
D: Cinnamoyl esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6114
Polymers57,1662
Non-polymers4442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-7 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.376, 153.391, 91.252
Angle α, β, γ (deg.)90.000, 127.396, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Cinnamoyl esterase


Mass: 28583.125 Da / Num. of mol.: 4 / Mutation: S106A
Source method: isolated from a genetically manipulated source
Details: Protein with tag sequence at N-terminal / Source: (gene. exp.) Lactobacillus acidophilus (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: A0A060IN49, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical
ChemComp-ZYC / ethyl (2E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enoate / ethyl ferulate


Mass: 222.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H14O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 3.17 Å3/Da / Density % sol: 61.18 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.02 M magnesium chloride, 0.1 M HEPES:NaOH pH 7.5 and 22 % (w/v) polyacrylic acid 5100

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 71881 / % possible obs: 98.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 18.68 Å2 / CC1/2: 0.994 / Net I/σ(I): 29.54
Reflection shellResolution: 2.19→2.23 Å / Num. unique obs: 3569 / CC1/2: 0.949

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Processing

Software
NameVersionClassification
REFMAC1.14_3260refinement
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PF8

3pf8


Resolution: 2.19→45.85 Å / SU ML: 0.2029 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 20.2632 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2137 3603 5.01 %
Rwork0.1858 68270 -
obs0.1872 71873 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.99 Å2
Refinement stepCycle: LAST / Resolution: 2.19→45.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7868 0 64 440 8372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01918105
X-RAY DIFFRACTIONf_angle_d2.044611003
X-RAY DIFFRACTIONf_chiral_restr0.11171211
X-RAY DIFFRACTIONf_plane_restr0.01261465
X-RAY DIFFRACTIONf_dihedral_angle_d21.41942952
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.220.21851050.19462272X-RAY DIFFRACTION85.32
2.22-2.250.23071280.19042626X-RAY DIFFRACTION98.29
2.25-2.280.25151390.18952606X-RAY DIFFRACTION98.39
2.28-2.320.21631620.19722599X-RAY DIFFRACTION98.4
2.32-2.350.24381590.19282614X-RAY DIFFRACTION98.47
2.35-2.390.24011590.19172573X-RAY DIFFRACTION98.56
2.39-2.430.21131380.1812621X-RAY DIFFRACTION98.47
2.43-2.480.1761280.19152636X-RAY DIFFRACTION98.57
2.48-2.520.24981310.1892664X-RAY DIFFRACTION98.66
2.52-2.570.21451330.19542609X-RAY DIFFRACTION98.78
2.57-2.630.21971430.19322601X-RAY DIFFRACTION98.78
2.63-2.690.21321330.19212640X-RAY DIFFRACTION98.82
2.69-2.760.25041210.19652669X-RAY DIFFRACTION99.08
2.76-2.830.23681530.20172633X-RAY DIFFRACTION99.11
2.83-2.920.22141400.18812627X-RAY DIFFRACTION99.07
2.92-3.010.23611520.18852614X-RAY DIFFRACTION99.07
3.01-3.120.18811490.19032656X-RAY DIFFRACTION99.05
3.12-3.240.19771470.19012654X-RAY DIFFRACTION99.33
3.24-3.390.23011390.19242621X-RAY DIFFRACTION99.03
3.39-3.570.17721130.17852686X-RAY DIFFRACTION99.26
3.57-3.790.19691410.17562643X-RAY DIFFRACTION99.43
3.79-4.090.18711470.1732663X-RAY DIFFRACTION99.33
4.09-4.50.21371330.16452655X-RAY DIFFRACTION99.11
4.5-5.150.19371220.17332688X-RAY DIFFRACTION99.57
5.15-6.480.23441470.20342686X-RAY DIFFRACTION99.82
6.48-45.850.21151410.18482714X-RAY DIFFRACTION99.37

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