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- PDB-7b7h: The glucuronoyl esterase OtCE15A R268A variant from Opitutus terr... -

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Basic information

Entry
Database: PDB / ID: 7b7h
TitleThe glucuronoyl esterase OtCE15A R268A variant from Opitutus terrae in complex with, and covalently linked to, D-glucuronate
ComponentsPutative acetyl xylan esterase
KeywordsHYDROLASE / CE15 / glucuronoyl esterase / glucuronate / glucuronic acid / biomass
Function / homology: / Glucuronyl esterase, fungi / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / metal ion binding / alpha-D-glucopyranuronic acid / GLYCINE / Putative acetyl xylan esterase
Function and homology information
Biological speciesOpitutus terrae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMazurkewich, S. / Larsbrink, J. / Lo Leggio, L.
Funding support Denmark, Sweden, 2items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF17OC0027698 Denmark
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Nat Commun / Year: 2022
Title: Mechanism and biomass association of glucuronoyl esterase: an alpha / beta hydrolase with potential in biomass conversion.
Authors: Zong, Z. / Mazurkewich, S. / Pereira, C.S. / Fu, H. / Cai, W. / Shao, X. / Skaf, M.S. / Larsbrink, J. / Lo Leggio, L.
History
DepositionDec 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative acetyl xylan esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,20731
Polymers46,0621
Non-polymers2,14530
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint34 kcal/mol
Surface area14180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.333, 47.298, 51.112
Angle α, β, γ (deg.)61.947, 67.920, 88.272
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Putative acetyl xylan esterase


Mass: 46062.434 Da / Num. of mol.: 1 / Mutation: R268A
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 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1ZMF4
#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.: 1 / 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 , 5 types, 140 molecules

#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H5NO2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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 Å3/Da / Density % sol: 38.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus screen consisting of 0.1 M buffer system 1 (imidazole and MES), 30% precipitant mix 2 (ethylene glycol and PEG 8000) and amino acid additives (L-Glutamate, Alanine (racemic); ...Details: Morpheus screen consisting of 0.1 M buffer system 1 (imidazole and MES), 30% precipitant mix 2 (ethylene glycol and PEG 8000) and amino acid additives (L-Glutamate, Alanine (racemic); Glycine; Lysine HCl (racemic); Serine (racemic)). Soaking was carried out in a saturated solution of Bnz-GlcA in 10% DMSO and 90% mother liquor for 30 seconds before being flash frozen.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 1.008 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 1.796→43.15 Å / Num. obs: 32171 / % possible obs: 96.62 % / Redundancy: 3.6 % / Biso Wilson estimate: 25.74 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.1202 / Net I/σ(I): 6.84
Reflection shellResolution: 1.796→1.861 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.256 / Mean I/σ(I) obs: 0.95 / Num. unique obs: 3093 / CC1/2: 0.461 / % possible all: 92.99

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GS0

6gs0


Resolution: 1.8→43.15 Å / SU ML: 0.2462 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.5936
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2224 1988 6.18 %
Rwork0.1826 30164 -
obs0.1851 32152 96.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.54 Å2
Refinement stepCycle: LAST / Resolution: 1.8→43.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2868 0 126 111 3105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00693068
X-RAY DIFFRACTIONf_angle_d0.8974146
X-RAY DIFFRACTIONf_chiral_restr0.054431
X-RAY DIFFRACTIONf_plane_restr0.008545
X-RAY DIFFRACTIONf_dihedral_angle_d14.37751079
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.38381350.37062071X-RAY DIFFRACTION91.92
1.84-1.890.33581430.32312127X-RAY DIFFRACTION95.38
1.89-1.950.29941350.27652125X-RAY DIFFRACTION96.05
1.95-2.010.25941480.25862159X-RAY DIFFRACTION96.65
2.01-2.080.26691380.21932132X-RAY DIFFRACTION96.19
2.08-2.160.23881460.19882161X-RAY DIFFRACTION96.65
2.16-2.260.24611390.18622184X-RAY DIFFRACTION96.99
2.26-2.380.21751420.16282147X-RAY DIFFRACTION96.83
2.38-2.530.23521370.17132167X-RAY DIFFRACTION97.17
2.53-2.730.23891460.16952168X-RAY DIFFRACTION97.88
2.73-30.20591530.15862194X-RAY DIFFRACTION97.87
3-3.440.19951390.15332176X-RAY DIFFRACTION98.05
3.44-4.330.20171420.15522177X-RAY DIFFRACTION97.19
4.33-43.150.19091450.17642176X-RAY DIFFRACTION97.97

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