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- PDB-8i5o: Crystal structure of TxGH116 D593A acid/base mutant from Thermoan... -

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Basic information

Entry
Database: PDB / ID: 8i5o
TitleCrystal structure of TxGH116 D593A acid/base mutant from Thermoanaerobacterium xylanolyticum
Componentsbeta-glucosidase
KeywordsHYDROLASE
Function / homology
Function and homology information


glucosylceramidase / glucosylceramide catabolic process / glucosylceramidase activity / beta-glucosidase 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
Biological speciesThermoanaerobacterium xylanolyticum LX-11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9744
Polymers91,7501
Non-polymers2243
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area26320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.199, 54.376, 83.378
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein beta-glucosidase


Mass: 91750.172 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
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
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: 2.22 Å3/Da / Density % sol: 44.62 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.24 M AMMONIUM SULFATE, 21% 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: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 37034 / % possible obs: 99.9 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.063 / Rrim(I) all: 0.157 / Rsym value: 0.108 / Χ2: 0.945 / Net I/σ(I): 12.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3653 / CC1/2: 0.777 / CC star: 0.935 / Rpim(I) all: 0.317 / Rrim(I) all: 0.732 / Rsym value: 0.603 / Χ2: 0.966 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement

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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: 2.3→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.756 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.347 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 1779 4.8 %RANDOM
Rwork0.173 ---
obs0.1754 34970 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.11 Å2 / Biso mean: 33.299 Å2 / Biso min: 18.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0 Å2-0 Å2
2--0.08 Å2-0 Å2
3---0.24 Å2
Refinement stepCycle: final / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6206 0 13 278 6497
Biso mean--48.96 35.23 -
Num. residues----769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.026421
X-RAY DIFFRACTIONr_bond_other_d0.0020.025857
X-RAY DIFFRACTIONr_angle_refined_deg1.1561.9328703
X-RAY DIFFRACTIONr_angle_other_deg0.871313524
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.085773
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30125.275309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.37151078
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1781512
X-RAY DIFFRACTIONr_chiral_restr0.070.2879
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027328
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021528
LS refinement shellResolution: 2.3→2.359 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 141 -
Rwork0.249 2405 -
all-2546 -
obs--95 %

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