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- PDB-6t0e: The glucuronoyl esterase OtCE15A S267A variant from Opitutus terr... -

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Basic information

Entry
Database: PDB / ID: 6t0e
TitleThe glucuronoyl esterase OtCE15A S267A variant from Opitutus terrae in complex with benzyl D-glucuronoate and D-glucuronate
Componentsglucuronoyl esterase OtCE15A
KeywordsHYDROLASE / Esterase / Complex / Biomass
Function / homologyGlucuronyl esterase, fungi / Alpha/Beta hydrolase fold / metal ion binding / alpha-D-glucopyranuronic acid / benzyl alpha-D-glucopyranuronate / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / trimethylamine oxide / Putative acetyl xylan esterase
Function and homology information
Biological speciesOpitutus terrae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsMazurkewich, S. / Navarro Poulsen, J.C. / Larsbrink, J. / Lo Leggio, L.
Funding support Sweden, Denmark, 2items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
Novo Nordisk FoundationNNF17OC0027698 Denmark
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structural and biochemical studies of the glucuronoyl esteraseOtCE15A illuminate its interaction with lignocellulosic components.
Authors: Mazurkewich, S. / Poulsen, J.N. / Lo Leggio, L. / Larsbrink, J.
History
DepositionOct 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: 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
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: glucuronoyl esterase OtCE15A
B: glucuronoyl esterase OtCE15A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,60665
Polymers92,2652
Non-polymers5,34163
Water7,422412
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A: glucuronoyl esterase OtCE15A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,45138
Polymers46,1331
Non-polymers3,31837
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: glucuronoyl esterase OtCE15A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,15527
Polymers46,1331
Non-polymers2,02226
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.719, 87.611, 173.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein glucuronoyl esterase OtCE15A


Mass: 46132.547 Da / Num. of mol.: 2 / Mutation: S267A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Opitutus terrae (strain DSM 11246 / JCM 15787 / PB90-1) (bacteria)
Strain: DSM 11246 / JCM 15787 / PB90-1 / Gene: Oter_0116 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1ZMF4

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Sugars , 2 types, 3 molecules

#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: isolated from a genetically manipulated source
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
#4: Sugar ChemComp-M55 / benzyl alpha-D-glucopyranuronate / Benzyl D-glucuronoate


Type: D-saccharide, alpha linking / Mass: 284.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H16O7 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 9 types, 472 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#10: Chemical
ChemComp-TMO / trimethylamine oxide


Mass: 75.110 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H9NO
#11: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.14 Å3/Da / Density % sol: 42.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Enzyme mixed 50/50 with reservoir solution containing JCSG+ screen solution G4: 0.2 M Trimethylamine N-oxide, 0.1 M Tris pH 8.5, and 20 % w/v PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.89→44.45 Å / Num. obs: 63514 / % possible obs: 98.98 % / Redundancy: 13.6 % / Biso Wilson estimate: 33.05 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1589 / Rpim(I) all: 0.04436 / Rrim(I) all: 0.1651 / Net I/σ(I): 12.25
Reflection shellResolution: 1.89→1.96 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 0.84 / Num. unique obs: 5944 / CC1/2: 0.403 / Rpim(I) all: 0.6206 / % possible all: 92

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHENIX1.15.2_3472phasing
PHENIX1.15.2_3472refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6gs0

6gs0


Resolution: 1.89→44.45 Å / SU ML: 0.2534 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.5575
RfactorNum. reflection% reflection
Rfree0.2155 1988 3.14 %
Rwork0.1622 --
obs0.1638 63362 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 39.74 Å2
Refinement stepCycle: LAST / Resolution: 1.89→44.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6081 0 344 412 6837
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01056649
X-RAY DIFFRACTIONf_angle_d1.1218976
X-RAY DIFFRACTIONf_chiral_restr0.0623930
X-RAY DIFFRACTIONf_plane_restr0.00791175
X-RAY DIFFRACTIONf_dihedral_angle_d22.80482389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.940.36541170.33993664X-RAY DIFFRACTION83.71
1.94-1.990.37331430.28044406X-RAY DIFFRACTION100
1.99-2.050.27291420.24854360X-RAY DIFFRACTION100
2.05-2.110.24871410.21464379X-RAY DIFFRACTION100
2.11-2.190.29171430.19154397X-RAY DIFFRACTION99.93
2.19-2.280.24811410.17834376X-RAY DIFFRACTION100
2.28-2.380.20991430.16824429X-RAY DIFFRACTION99.89
2.38-2.510.2111420.16784384X-RAY DIFFRACTION99.28
2.51-2.660.23471430.16234400X-RAY DIFFRACTION99.54
2.66-2.870.25321410.15724402X-RAY DIFFRACTION98.85
2.87-3.160.19791450.14914448X-RAY DIFFRACTION99.87
3.16-3.610.1791450.13624476X-RAY DIFFRACTION99.98
3.61-4.550.16291470.12524528X-RAY DIFFRACTION100
4.55-44.450.22711550.16774725X-RAY DIFFRACTION99.61

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