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- PDB-6gu8: Glucuronoyl Esterase from Solibacter usitatus -

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Basic information

Entry
Database: PDB / ID: 6gu8
TitleGlucuronoyl Esterase from Solibacter usitatus
ComponentsPutative acetyl xylan esterase
KeywordsHYDROLASE / Carbohydrate Esterase
Function / homologyGlucuronyl esterase, fungi / Alpha/Beta hydrolase fold / DI(HYDROXYETHYL)ETHER / Putative acetyl xylan esterase
Function and homology information
Biological speciesCandidatus Solibacter usitatus Ellin6076 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01807823457 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 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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: Putative acetyl xylan esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,02912
Polymers44,2141
Non-polymers81511
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint37 kcal/mol
Surface area16080 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

#1: Protein Putative acetyl xylan esterase


Mass: 44213.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Solibacter usitatus Ellin6076 (bacteria)
Gene: Acid_4275 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q01YM8
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Reservoir composition: 0.02 M D-glucose, 0.02 M D-mannose, 0.02 M D-galactose, 0.02 M L-fucose, 0.02 M D-xylose, 0.02 M N-acetyl-D-glucosamine, 0.05 M Tris, 0.05 M BICINE, 20% v/v PEG500MME, ...Details: Reservoir composition: 0.02 M D-glucose, 0.02 M D-mannose, 0.02 M D-galactose, 0.02 M L-fucose, 0.02 M D-xylose, 0.02 M N-acetyl-D-glucosamine, 0.05 M Tris, 0.05 M BICINE, 20% v/v PEG500MME, 10% w/v PEG20000 Drop size and composition: Sitting drops of 0.3 ul were mixed in a protein:reservoir volume ratio of 1:1 using 23.6 mg/mL of SuCE15C-SeMet in 20 mM TRIS pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.018→47.29 Å / Num. obs: 59163 / % possible obs: 99.95 % / Redundancy: 2 % / Biso Wilson estimate: 32.6808653387 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0691 / Net I/σ(I): 9.27
Reflection shellResolution: 2.02→2.09 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4261 / Mean I/σ(I) obs: 1.35 / Num. unique obs: 5723 / CC1/2: 0.889 / % possible all: 99.65

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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: SAD / Resolution: 2.01807823457→47.2880572634 Å / SU ML: 0.302442641961 / Cross valid method: FREE R-VALUE / σ(F): 1.35372315283 / Phase error: 27.8375960532
RfactorNum. reflection% reflection
Rfree0.248590986642 956 3.23103961065 %
Rwork0.183738965461 --
obs0.185924125236 29588 99.9662139334 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.4221082505 Å2
Refinement stepCycle: LAST / Resolution: 2.01807823457→47.2880572634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3052 0 53 277 3382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01179686659183253
X-RAY DIFFRACTIONf_angle_d1.158070496274393
X-RAY DIFFRACTIONf_chiral_restr0.0584218648783442
X-RAY DIFFRACTIONf_plane_restr0.00817854120413577
X-RAY DIFFRACTIONf_dihedral_angle_d16.25284787781934
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0181-2.12450.3474193105121330.2947075544093954X-RAY DIFFRACTION99.7559189651
2.1245-2.25760.3176189359241340.2502534357084020X-RAY DIFFRACTION100
2.2576-2.43190.3083165953231330.2296849770724001X-RAY DIFFRACTION100
2.4319-2.67660.305643861051350.2164408343274031X-RAY DIFFRACTION100
2.6766-3.06380.2947608520531350.1923266624144074X-RAY DIFFRACTION100
3.0638-3.85980.222173060641390.1609026161774154X-RAY DIFFRACTION100
3.8598-47.3010.196742625681470.1493275218714398X-RAY DIFFRACTION100

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