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- PDB-7xrh: Feruloyl esterase from Lactobacillus acidophilus -

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Basic information

Entry
Database: PDB / ID: 7xrh
TitleFeruloyl esterase from Lactobacillus acidophilus
ComponentsCinnamoyl esterase
KeywordsHYDROLASE / Feruloyl esterase
Function / homologyDienelactone hydrolase / Dienelactone hydrolase family / Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / aminopeptidase activity / Alpha/Beta hydrolase fold / Cinnamoyl esterase
Function and homology information
Biological speciesLactobacillus acidophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHwang, J. / Lee, C.W. / Lee, J.H. / Do, H.
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
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

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Assembly

Deposited unit
A: Cinnamoyl esterase
B: Cinnamoyl esterase


Theoretical massNumber of molelcules
Total (without water)54,9762
Polymers54,9762
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-8 kcal/mol
Surface area17940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.188, 74.590, 123.367
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Cinnamoyl esterase


Mass: 27487.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Several parts of the structure which showed a weak electron density map were deleted.
Source: (gene. exp.) Lactobacillus acidophilus (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: A0A060IN49, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.06 Å3/Da / Density % sol: 40.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20 % (w/v) PEG MME 5000, 0.1 M Bis-Tris-HCl (pH 6.5)

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Data collection

DiffractionMean temperature: 100 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: Dec 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 20175 / % possible obs: 97.2 % / Redundancy: 6.8 % / Biso Wilson estimate: 37.4 Å2 / CC1/2: 0.954 / Net I/σ(I): 25.05
Reflection shellResolution: 2.3→2.34 Å / Mean I/σ(I) obs: 4.62 / Num. unique obs: 1031 / CC1/2: 0.928

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Processing

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

3pf8


Resolution: 2.3→41.06 Å / SU ML: 0.3024 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.3203 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2803 2000 9.95 %
Rwork0.2265 18110 -
obs0.2318 20110 96.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.02 Å2
Refinement stepCycle: LAST / Resolution: 2.3→41.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3624 0 0 66 3690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01163697
X-RAY DIFFRACTIONf_angle_d1.32385018
X-RAY DIFFRACTIONf_chiral_restr0.0779563
X-RAY DIFFRACTIONf_plane_restr0.0083664
X-RAY DIFFRACTIONf_dihedral_angle_d22.75241357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.3671230.28241117X-RAY DIFFRACTION84.41
2.35-2.420.3281480.27181333X-RAY DIFFRACTION99.87
2.42-2.490.35281450.27241312X-RAY DIFFRACTION99.86
2.49-2.570.30861460.26571324X-RAY DIFFRACTION100
2.57-2.660.30921440.25891313X-RAY DIFFRACTION100
2.66-2.770.33191490.26671341X-RAY DIFFRACTION99.87
2.77-2.890.29451460.24391330X-RAY DIFFRACTION100
2.89-3.050.32911460.24531314X-RAY DIFFRACTION100
3.05-3.240.30721490.23981347X-RAY DIFFRACTION99.93
3.24-3.490.27651470.21571335X-RAY DIFFRACTION99.87
3.49-3.840.2511200.21181090X-RAY DIFFRACTION80.94
3.84-4.390.25341370.19391243X-RAY DIFFRACTION92.12
4.39-5.530.27831390.20191253X-RAY DIFFRACTION90.57
5.53-41.060.22461610.21481458X-RAY DIFFRACTION99.82

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