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- PDB-6xyc: Truncated form of carbohydrate esterase from gut microbiota -

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Basic information

Entry
Database: PDB / ID: 6xyc
TitleTruncated form of carbohydrate esterase from gut microbiota
ComponentsAcetyl xylan esterase
KeywordsHYDROLASE / Acetyl xylan esterase / alpha/beta hydrolase
Function / homology4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPenttinen, L. / Hakulinen, N. / Master, E.
Funding supportEuropean Union, Finland, 2items
OrganizationGrant numberCountry
European Research Council (ERC)648925European Union
Academy of Finland292705 Finland
CitationJournal: Biotechnol Biofuels / Year: 2021
Title: Polysaccharide utilization loci-driven enzyme discovery reveals BD-FAE: a bifunctional feruloyl and acetyl xylan esterase active on complex natural xylans.
Authors: Hameleers, L. / Penttinen, L. / Ikonen, M. / Jaillot, L. / Faure, R. / Terrapon, N. / Deuss, P.J. / Hakulinen, N. / Master, E.R. / Jurak, E.
History
DepositionJan 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jun 16, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetyl xylan esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8732
Polymers31,6701
Non-polymers2031
Water3,405189
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: mass spectrometry, native gel electrophoresis, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint4 kcal/mol
Surface area10850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.560, 107.560, 44.378
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Acetyl xylan esterase


Mass: 31670.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-AES / 4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / AEBSF


Mass: 203.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10FNO2S / Comment: protease inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.1 Å3/Da / Density % sol: 41.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2 M Ammonium sulfate, 30 % PEG MME 5000, 0.1 M mes pH 6.0, protein concentration 12 mg/ml

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.85→29.84 Å / Num. obs: 22926 / % possible obs: 99.85 % / Redundancy: 6.984 % / Biso Wilson estimate: 27.03 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.146 / Net I/σ(I): 11.26
Reflection shellResolution: 1.85→1.96 Å / Num. unique obs: 6826 / CC1/2: 0.515

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6tkx

6tkx


Resolution: 1.85→29.83 Å / SU ML: 0.1895 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.5074
RfactorNum. reflection% reflection
Rfree0.2026 1147 5 %
Rwork0.1759 --
obs0.1773 22925 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29.76 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2155 0 12 189 2356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00462236
X-RAY DIFFRACTIONf_angle_d0.70053047
X-RAY DIFFRACTIONf_chiral_restr0.047336
X-RAY DIFFRACTIONf_plane_restr0.0044397
X-RAY DIFFRACTIONf_dihedral_angle_d2.54641784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.930.31611390.26962640X-RAY DIFFRACTION98.79
1.93-2.030.27351400.22362664X-RAY DIFFRACTION100
2.03-2.160.24841410.1972670X-RAY DIFFRACTION100
2.16-2.330.20921430.18062711X-RAY DIFFRACTION99.96
2.33-2.560.21281420.17052701X-RAY DIFFRACTION100
2.56-2.930.19271430.17262724X-RAY DIFFRACTION100
2.93-3.690.19251460.17012760X-RAY DIFFRACTION100
3.69-29.830.17841530.15882908X-RAY DIFFRACTION100

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