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- PDB-6sz4: The glucuronoyl esterase OtCE15A H408A variant from Opitutus terr... -

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Basic information

Entry
Database: PDB / ID: 6sz4
TitleThe glucuronoyl esterase OtCE15A H408A variant from Opitutus terrae in complex with, and covalently linked to, 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 / beta-D-glucopyranuronic acid / FORMIC ACID / Putative acetyl xylan esterase
Function and homology information
Biological speciesOpitutus terrae PB90-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 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 / 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.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)46,3223
Polymers46,0811
Non-polymers2402
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area490 Å2
ΔGint2 kcal/mol
Surface area15380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.104, 44.150, 50.179
Angle α, β, γ (deg.)76.095, 66.231, 70.854
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein glucuronoyl esterase OtCE15A


Mass: 46081.480 Da / Num. of mol.: 1 / Mutation: H408A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Opitutus terrae PB90-1 (bacteria) / Gene: Oter_0116 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1ZMF4
#2: Sugar ChemComp-BDP / beta-D-glucopyranuronic acid / beta-D-glucuronic acid / D-glucuronic acid / glucuronic acid


Type: D-saccharide, beta 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
DGlcpAbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranuronic acidCOMMON NAMEGMML 1.0
b-D-GlcpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcASNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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
Details: Protein mixed 50/50 with reservoir solution of 0.2 M Ammonium formate None 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.749→45.56 Å / Num. obs: 30662 / % possible obs: 95.48 % / Redundancy: 3.4 % / Biso Wilson estimate: 22.59 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.09829 / Rpim(I) all: 0.06242 / Rrim(I) all: 0.1169 / Net I/σ(I): 6.62
Reflection shellResolution: 1.749→1.812 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.8285 / Mean I/σ(I) obs: 1.53 / Num. unique obs: 2844 / CC1/2: 0.736 / Rpim(I) all: 0.5228 / Rrim(I) all: 0.9829 / % possible all: 88.67

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Processing

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

6gs0


Resolution: 1.75→45.56 Å / SU ML: 0.258 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 38.9229
RfactorNum. reflection% reflection
Rfree0.2836 2286 7.46 %
Rwork0.2136 --
obs0.2189 30624 95.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 38.37 Å2
Refinement stepCycle: LAST / Resolution: 1.75→45.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3075 0 15 109 3199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01153198
X-RAY DIFFRACTIONf_angle_d1.18124373
X-RAY DIFFRACTIONf_chiral_restr0.0603465
X-RAY DIFFRACTIONf_plane_restr0.0088583
X-RAY DIFFRACTIONf_dihedral_angle_d21.53561145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.52211220.43331567X-RAY DIFFRACTION84.11
1.79-1.830.49551410.40491756X-RAY DIFFRACTION94.33
1.83-1.870.46381420.3651792X-RAY DIFFRACTION95.41
1.87-1.920.36691450.34061740X-RAY DIFFRACTION94.58
1.92-1.980.39751380.30611760X-RAY DIFFRACTION95.33
1.98-2.050.33371450.28961764X-RAY DIFFRACTION94.98
2.05-2.120.34931400.26341777X-RAY DIFFRACTION95.52
2.12-2.20.33051460.24841781X-RAY DIFFRACTION96.21
2.2-2.30.30711480.2421799X-RAY DIFFRACTION96.29
2.3-2.420.32051450.21781787X-RAY DIFFRACTION96.55
2.42-2.580.30891420.2081774X-RAY DIFFRACTION96.23
2.58-2.780.24451460.20171818X-RAY DIFFRACTION97.23
2.78-3.060.2651440.21795X-RAY DIFFRACTION97.24
3.06-3.50.26111490.1951793X-RAY DIFFRACTION97.39
3.5-4.410.23271470.15881822X-RAY DIFFRACTION97.38
4.41-45.560.21211460.15511813X-RAY DIFFRACTION97.9

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