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- PDB-6tkx: Carbohydrate esterase from gut microbiota -

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Basic information

Entry
Database: PDB / ID: 6tkx
TitleCarbohydrate esterase from gut microbiota
ComponentsCarbohydrate esterase
KeywordsHYDROLASE / Carbohydrate esterase / alpha/beta hydrolase
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsPenttinen, L. / Hakulinen, N. / Master, R.E.
Funding support Finland, Sweden, 2items
OrganizationGrant numberCountry
Academy of Finland292705 Finland
Other private Sweden
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
DepositionNov 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbohydrate esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6442
Polymers32,5481
Non-polymers961
Water2,054114
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: light scattering, mass spectrometry, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-15 kcal/mol
Surface area11980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.460, 108.460, 44.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-604-

HOH

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Components

#1: Protein Carbohydrate esterase


Mass: 32548.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 41.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2 M Ammonium sulfate, 25% PEG MME 5000, 0.1 M mes pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.06→41.399 Å / Num. obs: 17093 / % possible obs: 99.9 % / Redundancy: 8.7 % / CC1/2: 0.6 / Rrim(I) all: 0.143 / Net I/σ(I): 10
Reflection shellResolution: 2.06→2.1 Å / Num. unique obs: 838 / CC1/2: 0.6 / Rrim(I) all: 1.5

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: 000)refinement
XDSdata reduction
XSCALEdata scaling
Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HXK, 4N5H, 5AO9, 2WTM, 3BXP, 3BJR, 4V2I, 2C7B, 4E15, 4Q3K, 3PFB, 3ZWQ, 5L2P, 3QH4, 5G5C, 5JD4, 4ZI5, 3F67, 5CML, 4WY8

3hxk

4n5h

5ao9

2wtm

3bxp

3bjr

4v2i

2c7b

4e15

4q3k

3pfb

3zwq

5l2p

3qh4

5g5c

5jd4

4zi5

3f67

5cml

4wy8


Resolution: 2.06→41.399 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.07
RfactorNum. reflection% reflection
Rfree0.2702 832 4.88 %
Rwork0.2054 --
obs0.2086 17055 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.06→41.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2212 0 5 115 2332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122279
X-RAY DIFFRACTIONf_angle_d1.1563107
X-RAY DIFFRACTIONf_dihedral_angle_d12.581345
X-RAY DIFFRACTIONf_chiral_restr0.058342
X-RAY DIFFRACTIONf_plane_restr0.008406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.18910.36731410.29842638X-RAY DIFFRACTION100
2.1891-2.35810.34081210.27162680X-RAY DIFFRACTION100
2.3581-2.59540.34061390.24532639X-RAY DIFFRACTION100
2.5954-2.97080.31231450.23872677X-RAY DIFFRACTION100
2.9708-3.74260.30791530.19632713X-RAY DIFFRACTION100
3.7426-41.3990.18951330.16792876X-RAY DIFFRACTION100

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