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- PDB-8j9f: Structure of STG-hydrolyzing beta-glucosidase 1 (PSTG1) -

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Basic information

Entry
Database: PDB / ID: 8j9f
TitleStructure of STG-hydrolyzing beta-glucosidase 1 (PSTG1)
ComponentsBeta-glucosidase
KeywordsHYDROLASE / GH3 family / sesaminol biosynthesis
Function / homology
Function and homology information


scopolin beta-glucosidase activity / beta-glucosidase activity / beta-glucosidase / 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 / Glycoside hydrolase, family 3, N-terminal domain superfamily ...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: 2.85 Å
AuthorsYanai, T. / Imaizumi, R. / Takahashi, Y. / Katsumura, E. / Yamamoto, M. / Nakayama, T. / Yamashita, S. / Takeshita, K. / Sakai, N. / Matsuura, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23H05470 Japan
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: To be published
Title: Structural insights into a bacterial beta-glucosidase that is capable of degrading sesaminol triglucoside to produce sesaminol
Authors: Yanai, T. / Imaizumi, R. / Nakayama, T. / Yamashita, S.
History
DepositionMay 3, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2024Provider: 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)346,7987
Polymers346,5224
Non-polymers2763
Water8,845491
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13560 Å2
ΔGint-68 kcal/mol
Surface area105810 Å2
2
A: Beta-glucosidase
B: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,4454
Polymers173,2612
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-33 kcal/mol
Surface area53240 Å2
MethodPISA
3
C: Beta-glucosidase
D: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,3533
Polymers173,2612
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-34 kcal/mol
Surface area53350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.300, 113.250, 158.660
Angle α, β, γ (deg.)71.468, 82.684, 79.830
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53A
63A
74A
84A
95A
105A
116A
126A

NCS domain segments:

Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: GLY / End label comp-ID: GLY / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 5 - 753 / Label seq-ID: 32 - 780

Dom-IDComponent-IDEns-ID
111
211
322
422
533
633
744
844
955
1055
1166
1266

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 491 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.3 Å3/Da / Density % sol: 62.72 %
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: Jun 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 832650 / % possible obs: 99.6 % / Redundancy: 8.46 % / CC1/2: 0.879 / Rrim(I) all: 0.619 / Net I/σ(I): 3.65
Reflection shellResolution: 2.85→3.02 Å / Redundancy: 8.25 % / Mean I/σ(I) obs: 1.33 / Num. unique obs: 131530 / CC1/2: 0.515 / Rrim(I) all: 1.661 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
PHENIX1.20.1-4487refinement
XDSdata reduction
XDSdata scaling
MOLREP11.9.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→47.6 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.807 / Cross valid method: FREE R-VALUE / ESU R Free: 0.411
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2817 5067 5.146 %Random selection
Rwork0.2317 93394 --
all0.234 ---
obs-98461 99.681 %-
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: 19.839 Å2
Baniso -1Baniso -2Baniso -3
1--1.229 Å2-0.629 Å2-0.115 Å2
2--1.792 Å21.404 Å2
3----0.033 Å2
Refinement stepCycle: LAST / Resolution: 2.85→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23104 0 18 491 23613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01223563
X-RAY DIFFRACTIONr_bond_other_d0.0020.01622454
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.64331864
X-RAY DIFFRACTIONr_angle_other_deg0.8561.56751785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04352981
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.6455145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.346104095
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.764101052
X-RAY DIFFRACTIONr_chiral_restr0.0720.23552
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0227617
X-RAY DIFFRACTIONr_gen_planes_other0.0050.025219
X-RAY DIFFRACTIONr_nbd_refined0.2120.24777
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2330.221226
X-RAY DIFFRACTIONr_nbtor_refined0.1860.211495
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.213388
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2603
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0670.215
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2430.219
X-RAY DIFFRACTIONr_nbd_other0.2440.234
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1150.22
X-RAY DIFFRACTIONr_mcbond_it1.5921.98211942
X-RAY DIFFRACTIONr_mcbond_other1.5921.98111941
X-RAY DIFFRACTIONr_mcangle_it2.6963.55814917
X-RAY DIFFRACTIONr_mcangle_other2.6963.55814918
X-RAY DIFFRACTIONr_scbond_it1.7022.14611621
X-RAY DIFFRACTIONr_scbond_other1.7022.14611622
X-RAY DIFFRACTIONr_scangle_it2.9553.86516947
X-RAY DIFFRACTIONr_scangle_other2.9553.86416948
X-RAY DIFFRACTIONr_lrange_it5.63923.59196861
X-RAY DIFFRACTIONr_lrange_other5.63823.60596777
X-RAY DIFFRACTIONr_ncsr_local_group_10.120.0522514
X-RAY DIFFRACTIONr_ncsr_local_group_20.1250.0522492
X-RAY DIFFRACTIONr_ncsr_local_group_30.1220.0522529
X-RAY DIFFRACTIONr_ncsr_local_group_40.1230.0522447
X-RAY DIFFRACTIONr_ncsr_local_group_50.1250.0522443
X-RAY DIFFRACTIONr_ncsr_local_group_60.120.0522755
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.119970.05007
12AX-RAY DIFFRACTIONLocal ncs0.119970.05007
23AX-RAY DIFFRACTIONLocal ncs0.125280.05007
24AX-RAY DIFFRACTIONLocal ncs0.125280.05007
35AX-RAY DIFFRACTIONLocal ncs0.122190.05007
36AX-RAY DIFFRACTIONLocal ncs0.122190.05007
47AX-RAY DIFFRACTIONLocal ncs0.123190.05007
48AX-RAY DIFFRACTIONLocal ncs0.123190.05007
59AX-RAY DIFFRACTIONLocal ncs0.124850.05007
510AX-RAY DIFFRACTIONLocal ncs0.124850.05007
611AX-RAY DIFFRACTIONLocal ncs0.119950.05007
612AX-RAY DIFFRACTIONLocal ncs0.119950.05007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.9240.3463770.3116904X-RAY DIFFRACTION99.8492
2.924-3.0030.3093350.296730X-RAY DIFFRACTION99.774
3.003-3.090.3583570.2896546X-RAY DIFFRACTION99.7976
3.09-3.1850.3363470.2746312X-RAY DIFFRACTION99.7155
3.185-3.2890.3313130.2666147X-RAY DIFFRACTION99.4458
3.289-3.4040.3143260.2635930X-RAY DIFFRACTION99.1442
3.404-3.5310.3073060.2465734X-RAY DIFFRACTION99.5222
3.531-3.6750.273320.2315522X-RAY DIFFRACTION99.8295
3.675-3.8370.2672660.2265323X-RAY DIFFRACTION99.7679
3.837-4.0230.2843090.2165019X-RAY DIFFRACTION99.794
4.023-4.2390.2472780.194796X-RAY DIFFRACTION99.8229
4.239-4.4940.2252490.1764565X-RAY DIFFRACTION99.8548
4.494-4.8010.232360.1784318X-RAY DIFFRACTION99.8028
4.801-5.1820.2261810.1774023X-RAY DIFFRACTION99.8812
5.182-5.6690.2612050.2033690X-RAY DIFFRACTION99.7184
5.669-6.3270.2661650.2313344X-RAY DIFFRACTION99.7725
6.327-7.2850.2991680.242945X-RAY DIFFRACTION99.8717
7.285-8.8710.2191380.2012479X-RAY DIFFRACTION99.7713
8.871-12.3330.2331150.1991947X-RAY DIFFRACTION99.8064
12.333-47.60.317640.2621120X-RAY DIFFRACTION98.5845

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