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- PDB-8i5q: Crystal structure of TxGH116 D593A acid/base mutant from Thermoan... -

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Basic information

Entry
Database: PDB / ID: 8i5q
TitleCrystal structure of TxGH116 D593A acid/base mutant from Thermoanaerobacterium xylanolyticum with laminaribiose
Componentsbeta-glucosidase
KeywordsHYDROLASE
Function / homology
Function and homology information


glucosylceramidase / glucosylceramide catabolic process / glucosylceramidase activity / carbohydrate metabolic process / membrane / metal ion binding
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
beta-laminaribiose / Glucosylceramidase
Similarity search - Component
Biological speciesThermoanaerobacterium xylanolyticum LX-11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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

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Assembly

Deposited unit
A: beta-glucosidase
B: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,5528
Polymers183,5002
Non-polymers1,0526
Water7,855436
1
A: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4205
Polymers91,7501
Non-polymers6704
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area25910 Å2
MethodPISA
2
B: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1333
Polymers91,7501
Non-polymers3822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area25350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.898, 100.625, 173.556
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein beta-glucosidase /


Mass: 91750.172 Da / Num. of mol.: 2 / 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
#2: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Antimicrobial / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-laminaribiose
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 440 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.24 M AMMONIUM SULFATE, 22% PEG 3350, 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: Oct 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 87398 / % possible obs: 99.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 12.8
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.891 / Mean I/σ(I) obs: 2 / Num. unique obs: 8654 / CC1/2: 0.748

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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: 2.2→40 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.921 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.273 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.241 4292 4.9 %RANDOM
Rwork0.1912 ---
obs0.1936 83029 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.71 Å2 / Biso mean: 35.451 Å2 / Biso min: 13.79 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å2-0 Å2
2--3.31 Å2-0 Å2
3----1.86 Å2
Refinement stepCycle: final / Resolution: 2.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12281 0 66 436 12783
Biso mean--46.69 33.82 -
Num. residues----1538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212769
X-RAY DIFFRACTIONr_bond_other_d00.0211500
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.93517350
X-RAY DIFFRACTIONr_angle_other_deg3.789326506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41351546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69625.215606
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.862152054
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3661524
X-RAY DIFFRACTIONr_chiral_restr0.0790.21778
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214635
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023043
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 291 -
Rwork0.282 5909 -
all-6200 -
obs--97.35 %

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