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- PDB-9lql: Structure of STG-hydrolyzing beta-glucosidase 1 (PSTG1) complexed... -

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Basic information

Entry
Database: PDB / ID: 9lql
TitleStructure of STG-hydrolyzing beta-glucosidase 1 (PSTG1) complexed with heptyl 1-thio-beta-D-glucopyranoside
ComponentsBeta-glucosidase
KeywordsHYDROLASE / GH3 family / sesaminol biosynthesis
Function / homology
Function and homology information


: / beta-glucosidase / beta-glucosidase activity / carbohydrate metabolic process
Similarity search - Function
: / Fibronectin type III-like domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Glycoside hydrolase, family 3, active site / Glycosyl hydrolases family 3 active site. / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal ...: / Fibronectin type III-like domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Glycoside hydrolase, family 3, active site / Glycosyl hydrolases family 3 active site. / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesPaenibacillus relictisesami (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsYanai, T. / Arai, A. / Takahashi, Y. / Imaizumi, R. / Takeshita, K. / Matsuura, H. / Sakai, N. / Takahashi, S. / Yamamoto, M. / Kataoka, K. ...Yanai, T. / Arai, A. / Takahashi, Y. / Imaizumi, R. / Takeshita, K. / Matsuura, H. / Sakai, N. / Takahashi, S. / Yamamoto, M. / Kataoka, K. / Nakayama, T. / Yamashita, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24KJ1191 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101070 (support number 2824) Japan
CitationJournal: To Be Published
Title: Structural and functional implications of the novel C-terminal domain and flexible loop in unique beta-glucosidase hydrolyzing sesaminol triglucoside to produce sesaminol
Authors: Yanai, T. / Arai, A. / Takahashi, Y. / Imaizumi, R. / Takeshita, K. / Matsuura, H. / Sakai, N. / Takahashi, S. / Yamamoto, M. / Kataoka, K. / Nakayama, T. / Yamashita, S.
History
DepositionJan 28, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-glucosidase
B: Beta-glucosidase
C: Beta-glucosidase
D: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)347,90913
Polymers346,5224
Non-polymers1,3889
Water1,964109
1
A: Beta-glucosidase
B: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,0086
Polymers173,2612
Non-polymers7474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Beta-glucosidase
D: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,9027
Polymers173,2612
Non-polymers6415
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.600, 112.040, 156.590
Angle α, β, γ (deg.)71.503, 82.829, 79.848
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 5 through 753)
d_2ens_1(chain "B" and (resid 5 through 56 or resid 65 through 705 or resid 715 through 753))
d_3ens_1(chain "C" and (resid 21 through 107 or resid 116 through 781 or resid 791 through 829))
d_4ens_1(chain "D" and (resid 5 through 56 or resid 65 through 705 or resid 715 through 753))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ARGARGGLYGLYAA5 - 75332 - 780
d_21ARGARGALAALABB5 - 5632 - 83
d_22ASPASPILEILEBB65 - 70592 - 732
d_23TYRTYRGLYGLYBB715 - 753742 - 780
d_31ARGARGALAALACC21 - 10732 - 83
d_32ASPASPILEILECC116 - 78192 - 732
d_33TYRTYRGLYGLYCC791 - 829742 - 780
d_41ARGARGALAALADD5 - 5632 - 83
d_42ASPASPILEILEDD65 - 70592 - 732
d_43TYRTYRGLYGLYDD715 - 753742 - 780

NCS oper:
IDCodeMatrixVector
1given(-0.9999982973, -0.00124658909814, -0.00136066595774), (-0.00184462202869, 0.696259771622, 0.717787522732), (5.25908683701E-5, 0.71778881047, -0.696260885587)0.581621369723, 0.37012423277, -0.843921015508
2given(0.999999691044, 9.59557533114E-5, 0.000780195125293), (9.28508193636E-5, -0.999992080425, 0.00397875173177), (0.000780570730599, -0.00397867806075, -0.999991780381)12.6904506781, -48.6541858887, -62.387020279
3given(-0.999990818315, -0.00266255982543, -0.00335768679447), (0.00426696818809, -0.690958714167, -0.722881628138), (-0.000395307368465, -0.722889318009, 0.69096373106)13.2138830754, -49.1095587632, -61.5215456955

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Components

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Protein / Sugars , 2 types, 7 molecules ABCD

#1: Protein
Beta-glucosidase


Mass: 86630.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus relictisesami (bacteria) / Gene: PSTG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D6RVX0
#2: Sugar ChemComp-HTG / heptyl 1-thio-beta-D-glucopyranoside / HEPTYL 1-THIOHEXOPYRANOSIDE / heptyl 1-thio-beta-D-glucoside / heptyl 1-thio-D-glucoside / heptyl 1-thio-glucoside


Type: D-saccharide / Mass: 294.408 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H26O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM

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Non-polymers , 4 types, 115 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 3.04 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 3000, imidazole, lithium sulfate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. obs: 57769 / % possible obs: 98.1 % / Redundancy: 4.7 % / Biso Wilson estimate: 16.95 Å2 / CC1/2: 0.781 / Net I/σ(I): 3.1
Reflection shellResolution: 3.35→3.55 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.51 / Num. unique obs: 9137 / CC1/2: 0.516 / Rrim(I) all: 0.516 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.35→45.85 Å / SU ML: 0.5074 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.3155
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2865 2870 4.97 %
Rwork0.2446 54874 -
obs0.2467 57744 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.25 Å2
Refinement stepCycle: LAST / Resolution: 3.35→45.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22967 0 86 109 23162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001623480
X-RAY DIFFRACTIONf_angle_d0.438831715
X-RAY DIFFRACTIONf_chiral_restr0.043525
X-RAY DIFFRACTIONf_plane_restr0.00354121
X-RAY DIFFRACTIONf_dihedral_angle_d12.82648846
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.601780048055
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.623379876171
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.557838799696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.35-3.410.36531510.29992769X-RAY DIFFRACTION96.37
3.41-3.470.34281460.29232651X-RAY DIFFRACTION96.61
3.47-3.540.32431230.27992748X-RAY DIFFRACTION97.85
3.54-3.610.34121670.27172751X-RAY DIFFRACTION98.32
3.61-3.690.35861290.2652691X-RAY DIFFRACTION97.68
3.69-3.770.32731410.25632725X-RAY DIFFRACTION96.92
3.77-3.870.33181570.25812706X-RAY DIFFRACTION97.08
3.87-3.970.30611360.2672725X-RAY DIFFRACTION98.11
3.97-4.090.30171370.25042790X-RAY DIFFRACTION99.19
4.09-4.220.29731330.23192804X-RAY DIFFRACTION99.29
4.22-4.370.22781500.20822720X-RAY DIFFRACTION99.14
4.37-4.550.22471640.21162737X-RAY DIFFRACTION98.91
4.55-4.750.22911140.21492829X-RAY DIFFRACTION99.16
4.75-50.22181540.21252776X-RAY DIFFRACTION99.49
5-5.320.27891420.22142770X-RAY DIFFRACTION99.05
5.32-5.730.28461440.24692747X-RAY DIFFRACTION99.01
5.73-6.30.30491410.25432771X-RAY DIFFRACTION98.91
6.3-7.210.28461450.24542757X-RAY DIFFRACTION98.67
7.21-9.070.22841700.21232714X-RAY DIFFRACTION98.2
9.07-45.850.21741260.22172693X-RAY DIFFRACTION96.08

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