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

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Basic information

Entry
Database: PDB / ID: 7dkw
TitleCrystal structure of TxGH116 E441G nucleophile mutant from Thermoanaerobacterium xylanolyticum with autocondensation products from alpha-fluoroglucoside.
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: 1.78 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
B: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,34013
Polymers183,4442
Non-polymers1,89611
Water23,0591280
1
A: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7056
Polymers91,7221
Non-polymers9835
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6357
Polymers91,7221
Non-polymers9136
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)179.214, 54.602, 164.550
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 , 1 types, 2 molecules AB

#1: Protein beta-glucosidase


Mass: 91722.117 Da / Num. of mol.: 2 / 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

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Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 1289 molecules

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


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1280 / 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: 2.21 Å3/Da / Density % sol: 44.42 %
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: 1.78→35 Å / Num. obs: 155241 / % possible obs: 99.4 % / Redundancy: 4.8 % / CC1/2: 0.998 / Net I/σ(I): 23
Reflection shellResolution: 1.78→1.84 Å / Num. unique obs: 14662 / CC1/2: 0.823

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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: 1.78→35 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.341 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1879 7479 4.9 %RANDOM
Rwork0.1577 ---
obs0.1592 144496 97.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.87 Å2 / Biso mean: 22.459 Å2 / Biso min: 7.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0 Å20 Å2
2--0.1 Å2-0 Å2
3---0.07 Å2
Refinement stepCycle: final / Resolution: 1.78→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12449 0 123 1280 13852
Biso mean--35.43 32.16 -
Num. residues----1540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213069
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211905
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.93817722
X-RAY DIFFRACTIONr_angle_other_deg0.9242.99627539
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41251565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28825.272624
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.921152192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7451524
X-RAY DIFFRACTIONr_chiral_restr0.0840.21790
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214857
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023091
LS refinement shellResolution: 1.78→1.826 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 443 -
Rwork0.232 8653 -
all-9096 -
obs--79.92 %

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