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- PDB-8i5s: Crystal structure of TxGH116 D593N acid/base mutant from Thermoan... -

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Basic information

Entry
Database: PDB / ID: 8i5s
TitleCrystal structure of TxGH116 D593N acid/base mutant from Thermoanaerobacterium xylanolyticum with 2-deoxy-2-fluoroglucoside
Componentsbeta-glucosidase
KeywordsHYDROLASE
Function / homology
Function and homology information


glucosylceramidase / glucosylceramide catabolic process / glucosylceramidase activity / beta-glucosidase activity / carbohydrate metabolic process / metal ion binding / membrane
Similarity search - Function
Glycosyl-hydrolase family 116, catalytic region / Beta-glucosidase GBA2-type / Glycosyl-hydrolase family 116, N-terminal / : / Glycosyl-hydrolase family 116, catalytic region / beta-glucosidase 2, glycosyl-hydrolase family 116 N-term / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
2-deoxy-2-fluoro-alpha-D-glucopyranose / Chem-NFG / Glucosylceramidase
Similarity search - Component
Biological speciesThermoanaerobacterium xylanolyticum LX-11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsPengthaisong, S. / Ketudat Cairns, J.R.
Funding support Thailand, 3items
OrganizationGrant numberCountry
Other governmentThailand Research Fund Thailand
Other governmentSuranaree University of Technology Thailand
Other governmentThailand Science Research and Innovation Thailand
CitationJournal: Acs Catalysis / Year: 2023
Title: Reaction Mechanism of Glycoside Hydrolase Family 116 Utilizes Perpendicular Protonation.
Authors: Pengthaisong, S. / Piniello, B. / Davies, G.J. / Rovira, C. / Ketudat Cairns, J.R.
History
DepositionJan 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,97119
Polymers91,7931
Non-polymers2,17818
Water10,935607
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-13 kcal/mol
Surface area25680 Å2
Unit cell
Length a, b, c (Å)177.192, 54.458, 83.094
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein beta-glucosidase


Mass: 91793.195 Da / Num. of mol.: 1 / Mutation: D593A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium xylanolyticum LX-11 (bacteria)
Strain: LX-11 / Gene: Thexy_2211 / Plasmid: PET30A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: F6BL85, beta-glucosidase

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Sugars , 2 types, 3 molecules

#2: Sugar ChemComp-G2F / 2-deoxy-2-fluoro-alpha-D-glucopyranose / 2-deoxy-2-fluoro-alpha-D-glucose / 2-deoxy-2-fluoro-D-glucose / 2-deoxy-2-fluoro-glucose


Type: D-saccharide, alpha linking / Mass: 182.147 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H11FO5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Glcp2fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#6: Sugar ChemComp-NFG / 2,4-dinitrophenyl 2-deoxy-2-fluoro-beta-D-glucopyranoside / 2,4-dinitrophenyl 2-deoxy-2-fluoro-beta-D-glucoside / 2,4-dinitrophenyl 2-deoxy-2-fluoro-D-glucoside / 2,4-dinitrophenyl 2-deoxy-2-fluoro-glucoside


Type: D-saccharide / Mass: 348.238 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C12H13FN2O9 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 4 types, 622 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / 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: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.18 M AMMONIUM SULFATE, 22% PEG 3000, 0.1 M MES, PH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→35 Å / Num. obs: 141041 / % possible obs: 98.6 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 25.8
Reflection shellResolution: 1.45→1.5 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 12918 / CC1/2: 0.787

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
Cootmodel building
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BVU

5bvu


Resolution: 1.45→35 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.112 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1758 6923 4.9 %RANDOM
Rwork0.1557 ---
obs0.1566 134044 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.62 Å2 / Biso mean: 18.256 Å2 / Biso min: 8.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20 Å2
2--1.27 Å2-0 Å2
3----0.7 Å2
Refinement stepCycle: final / Resolution: 1.45→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6221 0 142 607 6970
Biso mean--32.24 29.62 -
Num. residues----769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.026608
X-RAY DIFFRACTIONr_bond_other_d0.0020.026012
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.9498945
X-RAY DIFFRACTIONr_angle_other_deg0.915313904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3585785
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36125.365315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.984151096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.581512
X-RAY DIFFRACTIONr_chiral_restr0.0830.2911
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027478
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021554
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 488 -
Rwork0.258 8908 -
all-9396 -
obs--89.95 %

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