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- PDB-8qef: A carbohydrate esterase family 15 (CE15) glucuronoyl esterase fro... -

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Basic information

Entry
Database: PDB / ID: 8qef
TitleA carbohydrate esterase family 15 (CE15) glucuronoyl esterase from Phocaeicola ATCC 8482 bound to novel ligand.
ComponentsPutative acetyl xylan esterase
KeywordsHYDROLASE / Esterase / CE15 / Glucuronoyl Esterase / Bacteroidota
Function / homology: / Glucuronyl esterase, fungi / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / beta-D-galactopyranuronic acid / Putative acetyl xylan esterase
Function and homology information
Biological speciesPhocaeicola vulgatus ATCC 8482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsBanerjee, S. / Poulsen, J.N. / Mazurkewich, S. / Seveso, A. / Larsbrink, J. / Lo Leggio, L.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF17OC0027698 Denmark
CitationJournal: Appl.Environ.Microbiol. / Year: 2024
Title: Polysaccharide utilization loci from Bacteroidota encode CE15 enzymes with possible roles in cleaving pectin-lignin bonds.
Authors: Seveso, A. / Mazurkewich, S. / Banerjee, S. / Poulsen, J.-.C.N. / Lo Leggio, L. / Larsbrink, J.
History
DepositionAug 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative acetyl xylan esterase
B: Putative acetyl xylan esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,8787
Polymers97,4362
Non-polymers4425
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint11 kcal/mol
Surface area30040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.215, 59.163, 87.163
Angle α, β, γ (deg.)90.00, 101.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative acetyl xylan esterase


Mass: 48717.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phocaeicola vulgatus ATCC 8482 (bacteria)
Gene: BVU_0175 / Plasmid: pET28-a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A6KWT9
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Sugar ChemComp-GTR / beta-D-galactopyranuronic acid / beta-D-galacturonic acid / D-galacturonic acid / galacturonic acid


Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O7
IdentifierTypeProgram
DGalpAbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranuronic acidCOMMON NAMEGMML 1.0
b-D-GalpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalASNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 1.92 Å3/Da / Density % sol: 35.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6.0, 20 mM NaCl, and 20-24% (w/v) PEG 6000, soaked in 0.25 M neutralised galacturonic acid.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.16→85.43 Å / Num. obs: 28249 / % possible obs: 93 % / Redundancy: 6.8 % / CC1/2: 0.986 / Net I/σ(I): 6.7
Reflection shellResolution: 2.16→2.35 Å / Num. unique obs: 1413 / CC1/2: 0.476

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→85.43 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.895 / SU B: 9.007 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.993 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25151 1367 4.8 %RANDOM
Rwork0.17884 ---
obs0.18236 26881 70.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.823 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0 Å20.2 Å2
2---0.14 Å20 Å2
3---0.18 Å2
Refinement stepCycle: 1 / Resolution: 2.16→85.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6226 0 29 95 6350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0136503
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175747
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.658840
X-RAY DIFFRACTIONr_angle_other_deg1.2461.58113401
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6575794
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73522.918353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.195151028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7771532
X-RAY DIFFRACTIONr_chiral_restr0.0680.2795
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027364
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021412
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3333.3723140
X-RAY DIFFRACTIONr_mcbond_other2.3333.3723139
X-RAY DIFFRACTIONr_mcangle_it3.6155.0523928
X-RAY DIFFRACTIONr_mcangle_other3.6155.0523929
X-RAY DIFFRACTIONr_scbond_it2.7413.663363
X-RAY DIFFRACTIONr_scbond_other2.7413.663364
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4175.3584907
X-RAY DIFFRACTIONr_long_range_B_refined6.2138.7637448
X-RAY DIFFRACTIONr_long_range_B_other6.2138.777445
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 5811 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.460.5
medium thermal7.42
LS refinement shellResolution: 2.161→2.217 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.061 2 -
Rwork0.271 131 -
obs--4.61 %

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