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- PDB-6syr: The wild type glucuronoyl esterase OtCE15A from Opitutus terrae i... -

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Basic information

Entry
Database: PDB / ID: 6syr
TitleThe wild type glucuronoyl esterase OtCE15A from Opitutus terrae in complex with D-glucuronate
Componentsglucuronoyl esterase OtCE15A
KeywordsHYDROLASE / Esterase / Complex / Biomass
Function / homology: / Glucuronyl esterase, fungi / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / metal ion binding / alpha-D-glucopyranuronic acid / Putative acetyl xylan esterase
Function and homology information
Biological speciesOpitutus terrae PB90-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 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 1, 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 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._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 1.3Jan 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

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Assembly

Deposited unit
A: glucuronoyl esterase OtCE15A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3348
Polymers47,8451
Non-polymers4907
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-11 kcal/mol
Surface area15550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.215, 44.189, 50.172
Angle α, β, γ (deg.)75.776, 65.425, 70.847
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 glucuronoyl esterase OtCE15A


Mass: 47844.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Opitutus terrae PB90-1 (bacteria) / Gene: Oter_0116 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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: 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

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Non-polymers , 4 types, 233 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Based on the Morpheus screen from Molecular Dimensions: G12 - 0.1 M Carboxylic acids, 0.1 M Buffer System 3, pH 8.5, 50 % v/v Precipitant Mix 4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.918374 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: 0.918374 Å / Relative weight: 1
ReflectionResolution: 1.49→32.69 Å / Num. obs: 47249 / % possible obs: 91.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 21.11 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06132 / Rpim(I) all: 0.03731 / Rrim(I) all: 0.07189 / Net I/σ(I): 9.88
Reflection shellResolution: 1.49→1.543 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.416 / Mean I/σ(I) obs: 0.82 / Num. unique obs: 18505 / CC1/2: 0.656 / Rpim(I) all: 0.8315 / % possible all: 91.36

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHENIX1.15.2_3472refinement
XDSdata reduction
XDSdata scaling
PHENIX1.15.2_3472phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GS0

6gs0


Resolution: 1.49→32.69 Å / SU ML: 0.2318 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 34.9957
RfactorNum. reflection% reflection
Rfree0.223 3520 7.47 %
Rwork0.1828 --
obs0.1859 47109 91.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33.37 Å2
Refinement stepCycle: LAST / Resolution: 1.49→32.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3068 0 31 227 3326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00853252
X-RAY DIFFRACTIONf_angle_d1.04994445
X-RAY DIFFRACTIONf_chiral_restr0.0763469
X-RAY DIFFRACTIONf_plane_restr0.0076595
X-RAY DIFFRACTIONf_dihedral_angle_d18.47531177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.510.56721420.57131715X-RAY DIFFRACTION91.61
1.51-1.530.50131500.50871762X-RAY DIFFRACTION91.31
1.53-1.550.46361320.46341749X-RAY DIFFRACTION91.49
1.55-1.580.44931470.42331770X-RAY DIFFRACTION92.3
1.58-1.610.49961350.40341741X-RAY DIFFRACTION92.05
1.61-1.630.35971460.37721786X-RAY DIFFRACTION91.83
1.63-1.660.40191390.36261738X-RAY DIFFRACTION91.52
1.66-1.690.38421510.34031764X-RAY DIFFRACTION92.02
1.69-1.730.34241460.29381755X-RAY DIFFRACTION91.39
1.73-1.770.31661370.28321746X-RAY DIFFRACTION92.21
1.77-1.810.28251420.24991771X-RAY DIFFRACTION92.37
1.81-1.850.26261420.21661746X-RAY DIFFRACTION91.92
1.85-1.90.28161470.19821730X-RAY DIFFRACTION91.56
1.9-1.960.24781320.19131765X-RAY DIFFRACTION90.59
1.96-2.020.20941400.18391730X-RAY DIFFRACTION90.47
2.02-2.090.25571380.18811716X-RAY DIFFRACTION89.61
2.09-2.180.24761290.1671693X-RAY DIFFRACTION89.05
2.18-2.280.2281350.16881676X-RAY DIFFRACTION86.98
2.28-2.40.20381280.15771556X-RAY DIFFRACTION81.75
2.4-2.550.18941160.15591373X-RAY DIFFRACTION71.18
2.55-2.740.17751450.15681826X-RAY DIFFRACTION96.29
2.74-3.020.1911520.15411865X-RAY DIFFRACTION97.68
3.02-3.460.19071480.1471868X-RAY DIFFRACTION97.67
3.46-4.350.16041500.12621866X-RAY DIFFRACTION97.3
4.35-32.690.18641510.14221882X-RAY DIFFRACTION98.4

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