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

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Basic information

Entry
Database: PDB / ID: 6syv
TitleThe glucuronoyl esterase OtCE15A S267A variant 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 / beta-D-glucopyranuronic acid / alpha-D-glucopyranuronic acid / DI(HYDROXYETHYL)ETHER / Putative acetyl xylan esterase
Function and homology information
Biological speciesOpitutus terrae PB90-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 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 / 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.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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,54618
Polymers46,1331
Non-polymers1,41417
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint27 kcal/mol
Surface area15880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.507, 44.497, 50.367
Angle α, β, γ (deg.)76.433, 66.963, 70.218
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 , 1 types, 1 molecules A

#1: Protein glucuronoyl esterase OtCE15A


Mass: 46132.547 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 BL21(DE3) (bacteria) / References: UniProt: B1ZMF4

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Sugars , 2 types, 2 molecules

#4: 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
#5: 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

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Non-polymers , 4 types, 383 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 1.82 Å3/Da / Density % sol: 32.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Enzyme mixed 50/50 with reservoir solution containing Morpheus screen solution G12: 0.1 M Carboxylic acids (0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; ...Details: Enzyme mixed 50/50 with reservoir solution containing Morpheus screen solution G12: 0.1 M Carboxylic acids (0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.2M Sodium oxamate), 0.1 M Buffer System 3 pH 8.5 (Tris; BICINE), and 50 % v/v Precipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873127 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873127 Å / Relative weight: 1
ReflectionResolution: 1.12→36.22 Å / Num. obs: 102117 / % possible obs: 81.67 % / Redundancy: 3.3 % / Biso Wilson estimate: 13.27 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.08792 / Rpim(I) all: 0.05606 / Rrim(I) all: 0.1046 / Net I/σ(I): 6.12
Reflection shellResolution: 1.12→1.16 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.044 / Mean I/σ(I) obs: 0.76 / Num. unique obs: 4777 / CC1/2: 0.452 / Rpim(I) all: 0.6856 / Rrim(I) all: 1.255 / % possible all: 38.26

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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: 1.12→36.22 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.307
RfactorNum. reflection% reflection
Rfree0.1816 7637 7.48 %
Rwork0.1619 --
obs0.1634 102078 81.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.99 Å2
Refinement stepCycle: LAST / Resolution: 1.12→36.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3107 0 92 368 3567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00933435
X-RAY DIFFRACTIONf_angle_d1.18634675
X-RAY DIFFRACTIONf_chiral_restr0.082490
X-RAY DIFFRACTIONf_plane_restr0.0089623
X-RAY DIFFRACTIONf_dihedral_angle_d21.69651252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.12-1.130.45351060.4381332X-RAY DIFFRACTION34.29
1.13-1.150.44671230.40521512X-RAY DIFFRACTION39.46
1.15-1.160.4211280.37791567X-RAY DIFFRACTION41.13
1.16-1.170.36141450.33831797X-RAY DIFFRACTION45.75
1.17-1.190.31851460.32061794X-RAY DIFFRACTION47.46
1.19-1.210.35191710.32952110X-RAY DIFFRACTION53.89
1.21-1.220.32231870.31382306X-RAY DIFFRACTION60.23
1.22-1.240.30182090.31182574X-RAY DIFFRACTION66.39
1.24-1.260.34282320.31352854X-RAY DIFFRACTION74.9
1.26-1.280.31972840.3033512X-RAY DIFFRACTION90.51
1.28-1.30.29732930.29743612X-RAY DIFFRACTION93.4
1.3-1.330.31722910.26743582X-RAY DIFFRACTION93.24
1.33-1.350.27292940.25483610X-RAY DIFFRACTION93.91
1.35-1.380.25552900.2393588X-RAY DIFFRACTION93.4
1.38-1.410.24482950.22983633X-RAY DIFFRACTION94.08
1.41-1.440.24542960.22073654X-RAY DIFFRACTION94.38
1.44-1.480.23572960.19243649X-RAY DIFFRACTION94.83
1.48-1.520.18952940.17243668X-RAY DIFFRACTION95.42
1.52-1.560.19142930.16723657X-RAY DIFFRACTION95.34
1.56-1.620.20043010.16523685X-RAY DIFFRACTION95.38
1.62-1.670.19232980.15773722X-RAY DIFFRACTION95.58
1.67-1.740.16882990.15863662X-RAY DIFFRACTION95.58
1.74-1.820.17852920.15823673X-RAY DIFFRACTION95.5
1.82-1.920.17233000.14593653X-RAY DIFFRACTION95.23
1.92-2.040.16272940.14543668X-RAY DIFFRACTION95.03
2.04-2.190.14822950.1383692X-RAY DIFFRACTION95.29
2.19-2.410.16082950.1373699X-RAY DIFFRACTION95.57
2.41-2.760.15593000.13593633X-RAY DIFFRACTION94.84
2.76-3.480.14672830.13133585X-RAY DIFFRACTION92.94
3.48-36.220.1463070.12613758X-RAY DIFFRACTION97.37

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