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

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Basic information

Entry
Database: PDB / ID: 8qcl
TitleA carbohydrate esterase family 15 (CE15) glucuronoyl esterase from Phocaeicola vulgatus ATCC 8482
ComponentsPutative acetyl xylan esterase
KeywordsHYDROLASE / Esterase / CE15 / Glucuronoyl esterase / Bacteroidota
Function / homology: / Glucuronyl esterase, fungi / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / alpha-D-glucopyranuronic acid / DI(HYDROXYETHYL)ETHER / Putative acetyl xylan esterase
Function and homology information
Biological speciesPhocaeicola vulgatus ATCC 8482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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 27, 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)98,24013
Polymers97,4362
Non-polymers80511
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-80 kcal/mol
Surface area30130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.282, 59.525, 87.452
Angle α, β, γ (deg.)90.00, 101.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#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: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A6KWT9
#2: Sugar ChemComp-GCU / alpha-D-glucopyranuronic acid / alpha-D-glucuronic acid / D-glucuronic acid / glucuronic acid


Type: D-saccharide, alpha linking / Mass: 194.139 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10O7 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpAaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranuronic acidCOMMON NAMEGMML 1.0
a-D-GlcpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcASNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 287 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.36 %
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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9117 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9117 Å / Relative weight: 1
ReflectionResolution: 1.8→48.93 Å / Num. obs: 42976 / % possible obs: 94.8 % / Redundancy: 4.3 % / CC1/2: 0.996 / Net I/σ(I): 9
Reflection shellResolution: 1.838→1.999 Å / Num. unique obs: 2149 / CC1/2: 0.575

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→48.93 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.369 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 2128 5 %RANDOM
Rwork0.1723 ---
obs0.17528 40847 65.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.844 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0 Å2-0.02 Å2
2---0.03 Å20 Å2
3---0.21 Å2
Refinement stepCycle: 1 / Resolution: 1.84→48.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6225 0 44 278 6547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0136582
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175809
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.6528963
X-RAY DIFFRACTIONr_angle_other_deg1.2721.58213556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.245809
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8622.938354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.28151038
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3751532
X-RAY DIFFRACTIONr_chiral_restr0.070.2809
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027485
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021427
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_it1.7382.6183182
X-RAY DIFFRACTIONr_mcbond_other1.7332.6173181
X-RAY DIFFRACTIONr_mcangle_it2.7273.9143994
X-RAY DIFFRACTIONr_mcangle_other2.7283.9153995
X-RAY DIFFRACTIONr_scbond_it2.3482.8813400
X-RAY DIFFRACTIONr_scbond_other2.3472.8823401
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7984.2084965
X-RAY DIFFRACTIONr_long_range_B_refined5.5430.2457602
X-RAY DIFFRACTIONr_long_range_B_other5.4830.2017561
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: 5689 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.460.5
medium thermal5.22
LS refinement shellResolution: 1.84→1.885 Å
RfactorNum. reflection% reflection
Rfree0.321 10 -
Rwork0.294 250 -
obs--5.38 %

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