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- PDB-7dkx: Crystal structure of TxGH116 E441G nucleophile mutant from Thermo... -

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Basic information

Entry
Database: PDB / ID: 7dkx
TitleCrystal structure of TxGH116 E441G nucleophile mutant from Thermoanaerobacterium xylanolyticum with cellobiose
Componentsbeta-glucosidase
KeywordsHYDROLASE / beta-glucosidase / nucleophile mutant
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
Biological speciesThermoanaerobacterium xylanolyticum LX-11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPengthaisong, S. / Ketudat Cairns, J.R.
Funding support Thailand, 2items
OrganizationGrant numberCountry
Other privateThailand Research Fund Thailand
Other privateSuranaree University of Technology Thailand
CitationJournal: Arch.Biochem.Biophys. / Year: 2021
Title: Structural basis for transglycosylation in glycoside hydrolase family GH116 glycosynthases.
Authors: Pengthaisong, S. / Hua, Y. / Ketudat Cairns, J.R.
History
DepositionNov 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,30216
Polymers91,7221
Non-polymers1,58015
Water12,322684
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)177.556, 54.424, 83.137
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: 91722.117 Da / Num. of mol.: 1 / Mutation: E441G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium xylanolyticum LX-11 (bacteria)
Strain: LX-11 / Gene: Thexy_2211 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: F6BL85, beta-glucosidase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 684 / 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: 2.21 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.24 M AMMONIUM SULFATE, 20% 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: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→89 Å / Num. obs: 89598 / % possible obs: 99.6 % / Redundancy: 5.5 % / CC1/2: 0.999 / Net I/σ(I): 28.3
Reflection shellResolution: 1.7→1.76 Å / Num. unique obs: 8544 / CC1/2: 0.911

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Processing

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

5bvu


Resolution: 1.7→88.78 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.756 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.18 4344 4.9 %RANDOM
Rwork0.153 ---
obs0.1543 84019 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 52.29 Å2 / Biso mean: 15.87 Å2 / Biso min: 6.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--0.18 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: final / Resolution: 1.7→88.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6216 0 102 684 7002
Biso mean--31.12 27.77 -
Num. residues----769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.026582
X-RAY DIFFRACTIONr_bond_other_d0.0020.026009
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.9448911
X-RAY DIFFRACTIONr_angle_other_deg0.917313901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3515788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.425.365315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94151101
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.781512
X-RAY DIFFRACTIONr_chiral_restr0.0810.2908
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027461
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021547
LS refinement shellResolution: 1.7→1.74 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.237 268 -
Rwork0.222 4948 -
obs--79.03 %

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