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

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Basic information

Entry
Database: PDB / ID: 6syu
TitleThe wild type glucuronoyl esterase OtCE15A from Opitutus terrae in complex with xylobiose
Componentsglucuronoyl esterase OtCE15A
KeywordsHYDROLASE / Esterase / Complex / Biomass
Function / homology: / Glucuronyl esterase, fungi / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / metal ion binding / 4beta-beta-xylobiose / Putative acetyl xylan esterase
Function and homology information
Biological speciesOpitutus terrae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 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 / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
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

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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)47,24210
Polymers46,1491
Non-polymers1,0939
Water11,277626
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-7 kcal/mol
Surface area15640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.686, 44.340, 50.979
Angle α, β, γ (deg.)77.236, 67.267, 70.577
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, 3 molecules A

#1: Protein glucuronoyl esterase OtCE15A


Mass: 46148.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Opitutus terrae (bacteria) / Gene: Oter_0116 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1ZMF4
#2: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 282.245 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 4beta-beta-xylobiose
DescriptorTypeProgram
DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a212h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 633 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.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 626 / 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: 1.85 Å3/Da / Density % sol: 33.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Enzyme mixed 50/50 with reservoir solution containing Morpheus screen solution C12: 0.09 M NPS (0.3M Sodium nitrate, 0.3 Sodium phosphate dibasic, 0.3M Ammonium sulfate), 0.1 M Buffer System ...Details: Enzyme mixed 50/50 with reservoir solution containing Morpheus screen solution C12: 0.09 M NPS (0.3M Sodium nitrate, 0.3 Sodium phosphate dibasic, 0.3M Ammonium sulfate), 0.1 M Buffer System 3 pH 8.5 (Tris; BICINE), 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: MAX IV / Beamline: BioMAX / Wavelength: 0.91837 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91837 Å / Relative weight: 1
ReflectionResolution: 1.33→41.58 Å / Num. obs: 57996 / % possible obs: 77 % / Redundancy: 3.5 % / Biso Wilson estimate: 10.69 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.04829 / Rpim(I) all: 0.02988 / Rrim(I) all: 0.05696 / Net I/σ(I): 15.38
Reflection shellResolution: 1.33→1.38 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.1664 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 1682 / CC1/2: 0.942 / Rpim(I) all: 0.1456 / Rrim(I) all: 0.2221 / % possible all: 22.3

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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: 1.33→41.58 Å / SU ML: 0.0777 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 16.6533
RfactorNum. reflection% reflection
Rfree0.1446 4338 7.48 %
Rwork0.1195 --
obs0.1214 57992 76.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 14.94 Å2
Refinement stepCycle: LAST / Resolution: 1.33→41.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3106 0 72 626 3804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00823419
X-RAY DIFFRACTIONf_angle_d1.02074669
X-RAY DIFFRACTIONf_chiral_restr0.0755489
X-RAY DIFFRACTIONf_plane_restr0.0076626
X-RAY DIFFRACTIONf_dihedral_angle_d19.23741260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.350.2343200.1823250X-RAY DIFFRACTION10.71
1.35-1.360.2483480.1722581X-RAY DIFFRACTION24.91
1.36-1.380.1689560.16698X-RAY DIFFRACTION29.99
1.38-1.40.1993630.1546780X-RAY DIFFRACTION34.18
1.4-1.420.1856730.1487902X-RAY DIFFRACTION38.28
1.42-1.440.185800.1514996X-RAY DIFFRACTION43.01
1.44-1.460.1837880.14461092X-RAY DIFFRACTION46.83
1.46-1.480.17661020.14591246X-RAY DIFFRACTION53.64
1.48-1.50.16421040.13961368X-RAY DIFFRACTION58.53
1.5-1.530.15431330.13751500X-RAY DIFFRACTION65.01
1.53-1.550.16681370.13451696X-RAY DIFFRACTION72.65
1.55-1.580.17261650.13762013X-RAY DIFFRACTION86.95
1.58-1.610.16571670.13012220X-RAY DIFFRACTION95.48
1.61-1.640.15831830.1282240X-RAY DIFFRACTION95.09
1.64-1.680.15991750.12752215X-RAY DIFFRACTION96.22
1.68-1.720.15551910.12612197X-RAY DIFFRACTION95.75
1.72-1.760.15421760.12862267X-RAY DIFFRACTION95.77
1.76-1.810.14581730.13272236X-RAY DIFFRACTION96.32
1.81-1.860.14891770.12542220X-RAY DIFFRACTION96.34
1.86-1.920.14951870.12342273X-RAY DIFFRACTION96.43
1.92-1.990.15691840.11552239X-RAY DIFFRACTION96.69
1.99-2.070.13721830.1122252X-RAY DIFFRACTION97.01
2.07-2.170.13951800.11092262X-RAY DIFFRACTION97.06
2.17-2.280.12321830.11162250X-RAY DIFFRACTION96.78
2.28-2.420.13461900.11052266X-RAY DIFFRACTION97.08
2.42-2.610.15531760.11272260X-RAY DIFFRACTION97.56
2.61-2.870.13771860.11492259X-RAY DIFFRACTION97.49
2.87-3.290.12811890.11252281X-RAY DIFFRACTION98.29
3.29-4.140.12541800.10442296X-RAY DIFFRACTION98.41
4.14-41.580.14771890.12792299X-RAY DIFFRACTION98.81

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