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- PDB-8q6s: A carbohydrate esterase family 15 (CE15) glucuronoyl esterase fro... -

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Basic information

Entry
Database: PDB / ID: 8q6s
TitleA carbohydrate esterase family 15 (CE15) glucuronoyl esterase from Phocaeicola vulgatus ATCC 8482
ComponentsPutative acetyl xylan esterase
KeywordsHYDROLASE / Esterase / CE15 / Glucuronoyl esterase / Bacteroidota
Function / homologyAlpha/Beta hydrolase fold / DI(HYDROXYETHYL)ETHER / Putative acetyl xylan esterase
Function and homology information
Biological speciesPhocaeicola vulgatus ATCC 8482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsMazurkewich, S. / Seveso, A. / Banerjee, S. / Lo Leggio, L. / Larsbrink, J.
Funding support Sweden, Denmark, 3items
OrganizationGrant numberCountry
Knut and Alice Wallenberg FoundationWallenberg Wood Science Center Sweden
Novo Nordisk FoundationNNF17OC0027698 Denmark
Novo Nordisk FoundationNNF21OC0071611 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 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _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)97,7836
Polymers97,4362
Non-polymers3474
Water5,062281
1
A: Putative acetyl xylan esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8473
Polymers48,7181
Non-polymers1292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative acetyl xylan esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9363
Polymers48,7181
Non-polymers2182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.382, 58.697, 89.539
Angle α, β, γ (deg.)90.000, 103.946, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A6KWT9
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.03 Å3/Da / Density % sol: 39.27 %
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: MAX IV / Beamline: BioMAX / Wavelength: 0.976254 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.99→48.64 Å / Num. obs: 50852 / % possible obs: 94.16 % / Redundancy: 5.4 % / Biso Wilson estimate: 39.02 Å2 / CC1/2: 0.998 / Net I/σ(I): 8.66
Reflection shellResolution: 1.99→2.061 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 0.64 / Num. unique obs: 4674 / CC1/2: 0.413 / % possible all: 85.19

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→48.64 Å / SU ML: 0.3513 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.9847
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.258 3551 7 %
Rwork0.1943 47184 -
obs0.1986 50735 93.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.29 Å2
Refinement stepCycle: LAST / Resolution: 1.99→48.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6361 0 21 281 6663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00976617
X-RAY DIFFRACTIONf_angle_d1.12058978
X-RAY DIFFRACTIONf_chiral_restr0.0633899
X-RAY DIFFRACTIONf_plane_restr0.00931181
X-RAY DIFFRACTIONf_dihedral_angle_d15.90292457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.010.47661170.44831533X-RAY DIFFRACTION77.65
2.01-2.040.4491300.4151704X-RAY DIFFRACTION85.3
2.04-2.070.41021290.37611732X-RAY DIFFRACTION87.17
2.07-2.110.42761330.35211765X-RAY DIFFRACTION88.48
2.11-2.140.33181350.33021796X-RAY DIFFRACTION89.56
2.14-2.180.34921340.31551780X-RAY DIFFRACTION89.23
2.18-2.220.3581350.29351797X-RAY DIFFRACTION90.32
2.22-2.260.32521360.27761832X-RAY DIFFRACTION90.9
2.26-2.310.31331380.26781822X-RAY DIFFRACTION91.55
2.31-2.360.32251390.25311851X-RAY DIFFRACTION92
2.36-2.410.34021380.24271844X-RAY DIFFRACTION93.01
2.41-2.470.32781430.24261886X-RAY DIFFRACTION93.85
2.47-2.540.30121420.22281882X-RAY DIFFRACTION94.76
2.54-2.610.28731430.2091915X-RAY DIFFRACTION95.37
2.61-2.70.31551460.21761937X-RAY DIFFRACTION95.68
2.7-2.790.31971460.21371934X-RAY DIFFRACTION96.7
2.79-2.90.28031480.21041958X-RAY DIFFRACTION97.77
2.9-3.040.27361490.21671989X-RAY DIFFRACTION99.12
3.04-3.20.27671520.20552010X-RAY DIFFRACTION99.68
3.2-3.40.25731510.19132007X-RAY DIFFRACTION99.77
3.4-3.660.22071510.17872013X-RAY DIFFRACTION99.54
3.66-4.030.22341520.15762024X-RAY DIFFRACTION99.59
4.03-4.610.21521510.13692018X-RAY DIFFRACTION99.86
4.61-5.810.19711540.13622049X-RAY DIFFRACTION99.95
5.81-48.640.19131590.14952106X-RAY DIFFRACTION99.65

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