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- PDB-9vmk: Crystal structure of TeGH116 from Thermosynechococcus elongatus w... -

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Basic information

Entry
Database: PDB / ID: 9vmk
TitleCrystal structure of TeGH116 from Thermosynechococcus elongatus with glucose
ComponentsTlr0193 protein
KeywordsHYDROLASE / TeGH116 / beta-glucosidase / Thermosynechococcus elongatus / cyanobacteria / glucose
Function / homology
Function and homology information


glucosylceramide catabolic process / glucosylceramidase activity / beta-glucosidase activity / carbohydrate metabolic process / 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
Similarity search - Domain/homology
beta-D-glucopyranose / L(+)-TARTARIC ACID / Tlr0193 protein
Similarity search - Component
Biological speciesThermosynechococcus vestitus BP-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBeagbandee, C. / Charoenwattanasatien, R. / Pengthaisong, S. / Kurisu, G. / Ketudat Cairns, J.R.
Funding support Thailand, Japan, 3items
OrganizationGrant numberCountry
Other governmentSuranaree University of Technology Thailand
Other governmentThailand Science Research and Innovation, and the National Science, Research and Innovation Fund (NSRF) under grant number 195669 (67A304000096) Thailand
Other governmentOsaka University Japan
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: The structure of Thermosynechococcus elongatus glycoside hydrolase family 116 beta-glucosidase shows the role of the noncatalytic N-terminal domain in controlling substrate specificity.
Authors: Beagbandee, C. / Charoenwattanasatien, R. / Pengthaisong, S. / Kurisu, G. / Ketudat Cairns, J.R.
History
DepositionJun 28, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tlr0193 protein
B: Tlr0193 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,49017
Polymers180,9202
Non-polymers1,56915
Water11,115617
1
A: Tlr0193 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,38310
Polymers90,4601
Non-polymers9239
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-12 kcal/mol
Surface area24830 Å2
MethodPISA
2
B: Tlr0193 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1077
Polymers90,4601
Non-polymers6476
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-12 kcal/mol
Surface area24960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)268.999, 55.094, 181.996
Angle α, β, γ (deg.)90.000, 131.858, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Tlr0193 protein / beta-glucosidase


Mass: 90460.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus vestitus BP-1 (bacteria)
Gene: tlr0193 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DMC7, beta-glucosidase
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 630 molecules

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


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 617 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.77 Å3/Da / Density % sol: 55.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 1M Potassium sodium tartrate tetrahydrate, 0.1M Bis-Tris propane pH 6.8

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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 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→26.535 Å / Num. obs: 132197 / % possible obs: 97.9 % / Redundancy: 3.8 % / CC1/2: 0.976 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.198 / Rrim(I) all: 0.28 / Χ2: 0.44 / Net I/σ(I): 5.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
10.95-26.523.20.02614.68080.9980.0260.0370.3188.5
2-2.033.91.0311.364400.4341.0311.4580.4496.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-2000data collection
autoPROCdata processing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→26.535 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.46 / SU ML: 0.114 / Cross valid method: FREE R-VALUE / ESU R: 0.148 / ESU R Free: 0.126
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1894 6491 4.91 %
Rwork0.1694 125704 -
all0.17 --
obs-132195 97.863 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.459 Å2
Baniso -1Baniso -2Baniso -3
1--0.703 Å2-0 Å2-0.546 Å2
2---0.67 Å20 Å2
3---0.902 Å2
Refinement stepCycle: LAST / Resolution: 2→26.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12475 0 100 617 13192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01213010
X-RAY DIFFRACTIONr_bond_other_d0.0040.01611574
X-RAY DIFFRACTIONr_angle_refined_deg1.8541.78717776
X-RAY DIFFRACTIONr_angle_other_deg0.6631.73426560
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.58651572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.829586
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.489101826
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.15210644
X-RAY DIFFRACTIONr_chiral_restr0.0960.21819
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215982
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023346
X-RAY DIFFRACTIONr_nbd_refined0.2130.22450
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2040.210521
X-RAY DIFFRACTIONr_nbtor_refined0.1860.26336
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.26335
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2617
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0280.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0820.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1450.210
X-RAY DIFFRACTIONr_nbd_other0.2170.292
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1250.28
X-RAY DIFFRACTIONr_mcbond_it2.0341.7586288
X-RAY DIFFRACTIONr_mcbond_other2.0241.7586288
X-RAY DIFFRACTIONr_mcangle_it2.9773.1597860
X-RAY DIFFRACTIONr_mcangle_other2.9793.1597861
X-RAY DIFFRACTIONr_scbond_it3.0352.0286722
X-RAY DIFFRACTIONr_scbond_other3.0352.0276721
X-RAY DIFFRACTIONr_scangle_it4.6133.589916
X-RAY DIFFRACTIONr_scangle_other4.6133.589916
X-RAY DIFFRACTIONr_lrange_it5.64917.0714600
X-RAY DIFFRACTIONr_lrange_other5.63117.02514522
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2-2.0520.2754380.25891550.25998740.9320.9497.15410.232
2.052-2.1080.2534160.24689210.24696480.9420.94596.77650.213
2.108-2.1680.2474770.23286170.23392980.9440.95297.8060.197
2.168-2.2340.2184880.21984050.21991000.9610.95897.72530.182
2.234-2.3070.2324310.21181340.21288410.9560.96196.87820.172
2.307-2.3880.2114100.279190.20185370.9650.96697.56350.16
2.388-2.4770.2043550.19577160.19582130.9640.96898.2710.155
2.477-2.5770.2073790.18874320.18979300.970.97198.49940.148
2.577-2.6910.2083710.17171250.17376580.9680.97797.88460.135
2.691-2.820.1813240.16268060.16372700.9770.9898.07430.127
2.82-2.9710.1863120.14765330.14969760.9770.98498.12210.119
2.971-3.1490.1672870.13361800.13565730.9820.98898.38730.112
3.149-3.3630.1643520.12757770.12962240.9820.98998.47360.111
3.363-3.6280.153240.12454290.12658280.9870.9998.71310.115
3.628-3.9660.1572940.12849600.1353570.9860.9998.07730.125
3.966-4.4220.1492480.13145410.13248450.9880.9998.84420.133
4.422-5.0830.1442070.14140840.14143560.9880.98998.50780.144
5.083-6.1690.2351550.18234970.18437020.9770.98698.64940.186
6.169-8.4970.1631290.15627740.15629340.9870.9998.94340.161
8.497-26.5350.164940.15616990.15618460.9890.99197.12890.181

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