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- PDB-7z2x: Wild-type ferulic acid esterase from Lactobacillus buchneri -

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Basic information

Entry
Database: PDB / ID: 7z2x
TitleWild-type ferulic acid esterase from Lactobacillus buchneri
ComponentsFerulic acid esterase
KeywordsHYDROLASE / Ferulic acid esterase / Lactobacillus buchneri / wild type
Function / homologyferuloyl esterase / feruloyl esterase activity / Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / aminopeptidase activity / Alpha/Beta hydrolase fold / Ferulic acid esterase
Function and homology information
Biological speciesLentilactobacillus buchneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 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
DepositionMar 1, 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
C: Ferulic acid esterase
D: Ferulic acid esterase


Theoretical massNumber of molelcules
Total (without water)126,7624
Polymers126,7624
Non-polymers00
Water15,835879
1
A: Ferulic acid esterase
B: Ferulic acid esterase


Theoretical massNumber of molelcules
Total (without water)63,3812
Polymers63,3812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-4 kcal/mol
Surface area20190 Å2
2
C: Ferulic acid esterase
D: Ferulic acid esterase


Theoretical massNumber of molelcules
Total (without water)63,3812
Polymers63,3812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-6 kcal/mol
Surface area20030 Å2
Unit cell
Length a, b, c (Å)47.830, 62.230, 94.850
Angle α, β, γ (deg.)103.05, 101.52, 92.80
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Ferulic acid esterase


Mass: 31690.588 Da / Num. of mol.: 4
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 879 / 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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 5.5, 0.2 M NaCl, 25% P3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96852 Å / Relative weight: 1
ReflectionResolution: 1.5→30.934 Å / Num. obs: 155659 / % possible obs: 93.5 % / Redundancy: 2.8 % / Biso Wilson estimate: 14.4 Å2 / CC1/2: 0.988 / Net I/σ(I): 6.7
Reflection shellResolution: 1.5→1.6 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 26396 / CC1/2: 0.528 / % possible all: 90

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: L. buchneri FAE

Resolution: 1.5→30.934 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2109 1986 1.28 %
Rwork0.1823 --
obs0.1826 155652 93.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→30.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8284 0 0 879 9163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058582
X-RAY DIFFRACTIONf_angle_d0.80811581
X-RAY DIFFRACTIONf_dihedral_angle_d16.2055055
X-RAY DIFFRACTIONf_chiral_restr0.0511230
X-RAY DIFFRACTIONf_plane_restr0.0051525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53750.30021290.26410518X-RAY DIFFRACTION90
1.5375-1.57910.25641530.244410583X-RAY DIFFRACTION90
1.5791-1.62560.25521380.23210660X-RAY DIFFRACTION91
1.6256-1.6780.2461350.223910876X-RAY DIFFRACTION92
1.678-1.7380.28391440.219810906X-RAY DIFFRACTION93
1.738-1.80760.24711360.206710943X-RAY DIFFRACTION94
1.8076-1.88980.23321450.197611072X-RAY DIFFRACTION94
1.8898-1.98950.22571580.190311046X-RAY DIFFRACTION94
1.9895-2.11410.23381260.179311197X-RAY DIFFRACTION95
2.1141-2.27730.20781500.172311181X-RAY DIFFRACTION95
2.2773-2.50630.22731390.179911245X-RAY DIFFRACTION96
2.5063-2.86880.24231470.180311184X-RAY DIFFRACTION96
2.8688-3.61350.18871440.166211119X-RAY DIFFRACTION95
3.6135-30.9340.14571420.156411136X-RAY DIFFRACTION95

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