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- PDB-6sz0: The glucuronoyl esterase OtCE15A H408A variant from Opitutus terrae -

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Basic information

Entry
Database: PDB / ID: 6sz0
TitleThe glucuronoyl esterase OtCE15A H408A variant from Opitutus terrae
Componentsglucuronoyl esterase OtCE15A
KeywordsHYDROLASE / Esterase / Complex / Biomass
Function / homology: / Glucuronyl esterase, fungi / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / metal ion binding / DI(HYDROXYETHYL)ETHER / Putative acetyl xylan esterase
Function and homology information
Biological speciesOpitutus terrae PB90-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 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 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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)46,6559
Polymers46,0811
Non-polymers5738
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-17 kcal/mol
Surface area15360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.197, 44.204, 50.154
Angle α, β, γ (deg.)76.310, 65.696, 70.744
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: 46081.480 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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Non-polymers , 6 types, 231 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 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: 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: 1.738→45.39 Å / Num. obs: 30758 / % possible obs: 94.21 % / Redundancy: 3.4 % / Biso Wilson estimate: 21.89 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.04631 / Rpim(I) all: 0.0293 / Rrim(I) all: 0.055 / Net I/σ(I): 14.6
Reflection shellResolution: 1.738→1.8 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.3377 / Mean I/σ(I) obs: 2.85 / Num. unique obs: 2499 / CC1/2: 0.945 / Rpim(I) all: 0.2129 / Rrim(I) all: 0.4005 / % possible all: 76.75

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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: 1.74→45.39 Å / SU ML: 0.1807 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 24.1081
RfactorNum. reflection% reflection
Rfree0.1921 2306 7.5 %
Rwork0.1423 --
obs0.1459 30727 94.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.06 Å2
Refinement stepCycle: LAST / Resolution: 1.74→45.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3063 0 35 223 3321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00893264
X-RAY DIFFRACTIONf_angle_d1.00574457
X-RAY DIFFRACTIONf_chiral_restr0.0573466
X-RAY DIFFRACTIONf_plane_restr0.0071597
X-RAY DIFFRACTIONf_dihedral_angle_d17.5751190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.780.34561000.32111238X-RAY DIFFRACTION66.3
1.78-1.820.28051450.22131785X-RAY DIFFRACTION93.73
1.82-1.860.26231450.2011785X-RAY DIFFRACTION95.31
1.86-1.910.27911450.18921786X-RAY DIFFRACTION94.56
1.91-1.970.25411450.17431788X-RAY DIFFRACTION94.62
1.97-2.030.22011460.16621798X-RAY DIFFRACTION95.11
2.03-2.110.20461450.15521789X-RAY DIFFRACTION95.46
2.11-2.190.25471450.13791796X-RAY DIFFRACTION95.05
2.19-2.290.17841470.13651805X-RAY DIFFRACTION95.64
2.29-2.410.1971470.13671812X-RAY DIFFRACTION96.17
2.41-2.560.19791490.13221838X-RAY DIFFRACTION96.69
2.56-2.760.15891490.12931826X-RAY DIFFRACTION97.05
2.76-3.040.17251480.1321828X-RAY DIFFRACTION97.73
3.04-3.480.17481490.12641843X-RAY DIFFRACTION98.03
3.48-4.380.15831510.11421859X-RAY DIFFRACTION97.76
4.38-45.390.18631500.14981845X-RAY DIFFRACTION97.99

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