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- PDB-6t0i: The wild type glucuronoyl esterase OtCE15A from Opitutus terrae i... -

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Basic information

Entry
Database: PDB / ID: 6t0i
TitleThe wild type glucuronoyl esterase OtCE15A from Opitutus terrae in complex with the aldotetrauronic acid XUX
Componentsglucuronoyl esterase OtCE15A
KeywordsHYDROLASE / Esterase / Complex / Biomass
Function / homologyAlpha/Beta hydrolase fold / : / DI(HYDROXYETHYL)ETHER / Putative acetyl xylan esterase
Function and homology information
Biological speciesOpitutus terrae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 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 3, 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: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / 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_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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)47,91621
Polymers46,1491
Non-polymers1,76720
Water4,648258
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint29 kcal/mol
Surface area15220 Å2
Unit cell
Length a, b, c (Å)43.406, 44.173, 50.237
Angle α, β, γ (deg.)75.800, 65.489, 70.984
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: 46148.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Opitutus terrae (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B1ZMF4, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Polysaccharide 4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-[beta-D-xylopyranose-(1-4)]beta-D-xylopyranose-(1-4)- ...4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-[beta-D-xylopyranose-(1-4)]beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 604.510 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,4,3/[a212h-1b_1-5][a2122A-1a_1-5_4*OC]/1-1-2-1/a4-b1_b2-c1_b4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(2+1)][a-D-GlcpA4Me]{}[(4+1)][b-D-Xylp]{}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 277 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / 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: Enzyme mixed 50/50 with reservoir solution containing Morpheus screen solution E8: 0.12 M Ethylene glycols (0.3M Diethylene glycol; 0.3M Triethylene glycol; 0.3M Tetraethylene glycol; 0.3M ...Details: Enzyme mixed 50/50 with reservoir solution containing Morpheus screen solution E8: 0.12 M Ethylene glycols (0.3M Diethylene glycol; 0.3M Triethylene glycol; 0.3M Tetraethylene glycol; 0.3M Pentaethylene glycol), 0.1 M Buffer System 2 pH 7.5 (Sodium HEPES; MOPS), 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: MASSIF-3 / Wavelength: 0.9677 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: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.53→32.49 Å / Num. obs: 42551 / % possible obs: 88.56 % / Redundancy: 3.7 % / Biso Wilson estimate: 22.42 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04434 / Rpim(I) all: 0.02683 / Rrim(I) all: 0.05191 / Net I/σ(I): 15.38
Reflection shellResolution: 1.53→1.59 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.33 / Mean I/σ(I) obs: 0.72 / Num. unique obs: 3634 / CC1/2: 0.508 / Rpim(I) all: 0.8103 / % possible all: 67.55

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Processing

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

6gs0


Resolution: 1.53→32.49 Å / SU ML: 0.266 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.8711
RfactorNum. reflection% reflection
Rfree0.1955 4168 9.9 %
Rwork0.1602 --
obs0.1638 42107 88.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.33 Å2
Refinement stepCycle: LAST / Resolution: 1.53→32.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3068 0 114 258 3440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01033299
X-RAY DIFFRACTIONf_angle_d1.15924474
X-RAY DIFFRACTIONf_chiral_restr0.063473
X-RAY DIFFRACTIONf_plane_restr0.0079590
X-RAY DIFFRACTIONf_dihedral_angle_d21.29061196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.550.8522150.8076220X-RAY DIFFRACTION14.7
1.55-1.570.39041370.38751317X-RAY DIFFRACTION91.74
1.57-1.590.34081480.33931308X-RAY DIFFRACTION91.46
1.59-1.610.36151380.3381335X-RAY DIFFRACTION92.64
1.61-1.630.4111470.38541290X-RAY DIFFRACTION91.06
1.63-1.650.38831450.37311300X-RAY DIFFRACTION91.92
1.65-1.680.39741330.33581350X-RAY DIFFRACTION92.23
1.68-1.70.33251530.29311304X-RAY DIFFRACTION90.95
1.7-1.730.32331440.27761310X-RAY DIFFRACTION92.55
1.73-1.760.28531400.25541313X-RAY DIFFRACTION91.15
1.76-1.790.27561400.24341306X-RAY DIFFRACTION92.22
1.79-1.820.25231470.21371317X-RAY DIFFRACTION90.59
1.82-1.850.2581410.20021294X-RAY DIFFRACTION92.05
1.85-1.890.21931450.1871312X-RAY DIFFRACTION90.33
1.89-1.930.23241440.20211280X-RAY DIFFRACTION90.36
1.93-1.980.22481420.1681291X-RAY DIFFRACTION90.75
1.98-2.030.20191400.16291291X-RAY DIFFRACTION89.83
2.03-2.080.22351450.16731263X-RAY DIFFRACTION88.78
2.08-2.140.22911430.1541263X-RAY DIFFRACTION88.48
2.14-2.210.19751300.15111269X-RAY DIFFRACTION88.04
2.21-2.290.20641400.14871210X-RAY DIFFRACTION85.07
2.29-2.380.15831210.13681167X-RAY DIFFRACTION80.96
2.38-2.490.18671100.1446968X-RAY DIFFRACTION68.97
2.49-2.620.20741400.14181242X-RAY DIFFRACTION86.43
2.62-2.790.1641540.12841401X-RAY DIFFRACTION97.68
2.79-30.16731560.13561396X-RAY DIFFRACTION97.98
3-3.310.14721580.12921392X-RAY DIFFRACTION98.29
3.31-3.780.15321580.12361406X-RAY DIFFRACTION98.3
3.78-4.760.13631540.11381421X-RAY DIFFRACTION98.75
4.76-32.490.19771600.16421403X-RAY DIFFRACTION98.49

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