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- PDB-7z2v: Ferulic acid esterase variant S114A from Lactobacillus buchneri -

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Basic information

Entry
Database: PDB / ID: 7z2v
TitleFerulic acid esterase variant S114A from Lactobacillus buchneri
ComponentsFerulic acid esterase
KeywordsHYDROLASE / Ferulic acid esterase / Lactobacillus buchneri / mutant S114
Function / homology: / feruloyl esterase / feruloyl esterase activity / Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold / metal ion binding / ACETATE ION / Ferulic acid esterase
Function and homology information
Biological speciesLentilactobacillus buchneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.45 Å
AuthorsMogodiniyai, K.K. / Reichenbach, T. / Kalyani, D.C. / Keskitalo, M.M. / Divne, C.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Other governmentFormas 2016-01449 Sweden
CitationJournal: Front Microbiol / Year: 2022
Title: Crystal structure of the feruloyl esterase from Lentilactobacillus buchneri reveals a novel homodimeric state.
Authors: Kasmaei, K.M. / Kalyani, D.C. / Reichenbach, T. / Jimenez-Quero, A. / Vilaplana, F. / Divne, C.
History
DepositionFeb 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 2024Group: 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: Ferulic acid esterase
B: Ferulic acid esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,72710
Polymers63,3492
Non-polymers3788
Water10,359575
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Gelfiltration used to confirm assembly
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.960, 79.960, 227.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Ferulic acid esterase


Mass: 31674.588 Da / Num. of mol.: 2 / Mutation: S114A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lentilactobacillus buchneri (bacteria) / Gene: faeA / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli B (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): T1 / References: UniProt: D7RU28, feruloyl esterase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 575 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.09 Å3/Da / Density % sol: 60.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium cacodylate pH 6.5, 0.2 M calcium acetate, 18% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97629 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97629 Å / Relative weight: 1
ReflectionResolution: 1.45→46.41 Å / Num. obs: 130627 / % possible obs: 99.3 % / Redundancy: 22.5 % / Biso Wilson estimate: 19.76 Å2 / CC1/2: 1 / Net I/σ(I): 25.1
Reflection shellResolution: 1.45→1.5 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 11811 / CC1/2: 0.526

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: L. buchneri FAE

Resolution: 1.45→40.14 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1771 2000 1.53 %
Rwork0.1673 128607 -
obs0.1675 130607 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.7 Å2 / Biso mean: 24.1526 Å2 / Biso min: 13.93 Å2
Refinement stepCycle: final / Resolution: 1.45→40.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4151 0 17 575 4743
Biso mean--28.15 32.97 -
Num. residues----525
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.490.33541330.33858515864894
1.49-1.530.29681390.29258973911299
1.53-1.570.28361420.252791299271100
1.57-1.620.23411410.214490679208100
1.62-1.680.20681420.189191229264100
1.68-1.750.19571420.175291429284100
1.75-1.830.17791430.176591779320100
1.83-1.920.19021420.174491579299100
1.92-2.040.18021440.164592089352100
2.04-2.20.19681430.16192299372100
2.2-2.420.17621440.166892869430100
2.42-2.770.16811450.166493129457100
2.77-3.490.16261460.161994399585100
3.49-40.140.15131540.1418985110005100

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