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- PDB-6gry: Glucuronoyl Esterase from Solibacter usitatus. -

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Basic information

Entry
Database: PDB / ID: 6gry
TitleGlucuronoyl Esterase from Solibacter usitatus.
ComponentsPutative acetyl xylan esterase
KeywordsHYDROLASE / Carbohydrate Esterase
Function / homology: / Glucuronyl esterase, fungi / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Putative acetyl xylan esterase
Function and homology information
Biological speciesCandidatus Solibacter usitatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.00033771874 Å
AuthorsLo Leggio, L. / Larsbrink, J. / Meland Knudsen, R. / Mazurkewich, S. / Navarro Poulsen, J.C.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Novo Nordisk Foundation NNF17OC0027698 Denmark
European UnionInterreg-programmet for Oresund-Kattegat-Skagerrak Denmark
CitationJournal: Biotechnol Biofuels / Year: 2018
Title: Biochemical and structural features of diverse bacterial glucuronoyl esterases facilitating recalcitrant biomass conversion.
Authors: Arnling Baath, J. / Mazurkewich, S. / Knudsen, R.M. / Poulsen, J.N. / Olsson, L. / Lo Leggio, L. / Larsbrink, J.
History
DepositionJun 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative acetyl xylan esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,82123
Polymers43,8381
Non-polymers1,98222
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint66 kcal/mol
Surface area16780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.579, 54.579, 284.112
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative acetyl xylan esterase


Mass: 43838.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Solibacter usitatus (bacteria)
Gene: Acid_4275 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q01YM8, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases

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Non-polymers , 5 types, 244 molecules

#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O

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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: 2.44 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 293.15 K
Details: Sitting drops of 0.3 ul were mixed in a protein:reservoir volume ratio of 3:1 using 20 mg/mL of SuCE15C in 20 mM TRIS pH 8.0
Method: vapor diffusion, sitting drop / pH: 8
Details: Reservoir composition: 0.3 M diethylene glycol, 0.3 M triethylene glycol, 0.3 M tetraethylene glycol, and 0.3 M pentaethylene glycol, 0.05 M Tris, 0.05 M BICINE, 20% v/v PEG500MME, 10% w/v PEG20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.899 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.899 Å / Relative weight: 1
ReflectionResolution: 2→47.29 Å / Num. obs: 29889 / % possible obs: 98.42 % / Redundancy: 8.1 % / Biso Wilson estimate: 32.6263807138 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1157 / Net I/σ(I): 11.58
Reflection shellResolution: 2→2.1 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.9087 / Mean I/σ(I) obs: 2.02 / Num. unique obs: 22245 / CC1/2: 0.49 / % possible all: 85.34

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Coot0.8.9 ELmodel building
XDSBUILT=20180126data reduction
PHENIX1.13_2998phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Undeposited model

Resolution: 2.00033771874→47.2880572634 Å / SU ML: 0.257824547651 / Cross valid method: FREE R-VALUE / σ(F): 1.36792898849 / Phase error: 24.4162887397
RfactorNum. reflection% reflection
Rfree0.239192649038 967 3.23519571763 %
Rwork0.187548481682 --
obs0.18926421186 29890 98.4292159252 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 43.6374272208 Å2
Refinement stepCycle: LAST / Resolution: 2.00033771874→47.2880572634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3061 0 130 222 3413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01258359295093296
X-RAY DIFFRACTIONf_angle_d1.206310500474413
X-RAY DIFFRACTIONf_chiral_restr0.0593420281137438
X-RAY DIFFRACTIONf_plane_restr0.00796197534052569
X-RAY DIFFRACTIONf_dihedral_angle_d15.39785432621944
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0003-2.10580.3047192799311250.2751642495433683X-RAY DIFFRACTION89.8325076669
2.1058-2.23770.328891809321360.2451070212614060X-RAY DIFFRACTION100
2.2377-2.41050.3085526336751380.2271427924174130X-RAY DIFFRACTION100
2.4105-2.65310.2534730159411370.2116625035234148X-RAY DIFFRACTION99.8834498834
2.6531-3.03690.2393575180771390.1932112616714182X-RAY DIFFRACTION99.9537358316
3.0369-3.82590.2132881873561420.1708205862854226X-RAY DIFFRACTION99.7943797121
3.8259-47.30130.2140636028611500.1597331054214494X-RAY DIFFRACTION99.3794136529

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