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- PDB-9u98: Glycoside hydrolase family 1 beta-glucosidase (E318G mutant) from... -

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Basic information

Entry
Database: PDB / ID: 9u98
TitleGlycoside hydrolase family 1 beta-glucosidase (E318G mutant) from Streptomyces griseus (sophorose complex)
ComponentsPutative beta-glucosidase
KeywordsHYDROLASE / beta-Glucosidase
Function / homologyGlycosyl hydrolase family 1 / Glycoside hydrolase family 1 / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycoside hydrolase superfamily / carbohydrate metabolic process / beta-D-glucopyranose / TRIETHYLENE GLYCOL / Putative beta-glucosidase
Function and homology information
Biological speciesStreptomyces griseus subsp. griseus NBRC 13350 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsKumakura, H. / Motouchi, S. / Nakai, H. / Nakajima, M.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20K05830 Japan
Japan Science and TechnologyJPMJSP2151 Japan
CitationJournal: Protein Sci. / Year: 2025
Title: A beta-1,2-glucan-associated glycoside hydrolase family 1 beta-glucosidase from Streptomyces griseus.
Authors: Kumakura, H. / Motouchi, S. / Kobayashi, K. / Inoue, M. / Kariuda, N. / Nakai, H. / Nakajima, M.
History
DepositionMar 27, 2025Deposition site: PDBJ / Processing site: PDBJ
SupersessionApr 16, 2025ID: 8KAQ
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative beta-glucosidase
B: Putative beta-glucosidase
C: Putative beta-glucosidase
D: Putative beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,28218
Polymers182,7624
Non-polymers2,51914
Water9,548530
1
A: Putative beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5966
Polymers45,6911
Non-polymers9065
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15960 Å2
MethodPISA
2
B: Putative beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2545
Polymers45,6911
Non-polymers5634
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-13 kcal/mol
Surface area15410 Å2
MethodPISA
3
C: Putative beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5615
Polymers45,6911
Non-polymers8704
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15520 Å2
MethodPISA
4
D: Putative beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8712
Polymers45,6911
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.793, 100.179, 96.048
Angle α, β, γ (deg.)90.000, 102.868, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Putative beta-glucosidase


Mass: 45690.605 Da / Num. of mol.: 4 / Mutation: E318G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseus subsp. griseus NBRC 13350 (bacteria)
Gene: SGR_2426 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1W1N0

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Sugars , 3 types, 6 molecules

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


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-2DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(2+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-glucopyranose-(1-2)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-2DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(2+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#6: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / 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 , 3 types, 538 molecules

#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris propane (pH 6.5), 0.3 M sodium formate, 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.13→46.824 Å / Num. obs: 93387 / % possible obs: 98.7 % / Redundancy: 3.4 % / CC1/2: 0.995 / Net I/σ(I): 10.4
Reflection shellResolution: 2.13→2.17 Å / Num. unique obs: 4558 / CC1/2: 0.637

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→46.818 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / Cross valid method: FREE R-VALUE / ESU R: 0.231 / ESU R Free: 0.189
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2278 4704 5.038 %
Rwork0.1808 88660 -
all0.183 --
obs-93364 98.515 %
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: 28.303 Å2
Baniso -1Baniso -2Baniso -3
1--0.007 Å20 Å20.002 Å2
2--0.002 Å20 Å2
3---0.003 Å2
Refinement stepCycle: LAST / Resolution: 2.13→46.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12145 0 162 530 12837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01212650
X-RAY DIFFRACTIONr_bond_other_d0.0020.01611332
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.80617294
X-RAY DIFFRACTIONr_angle_other_deg0.9261.7526025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88351553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.6585107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.492101767
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.72310605
X-RAY DIFFRACTIONr_chiral_restr0.0830.21882
X-RAY DIFFRACTIONr_chiral_restr_other0.0010.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215409
X-RAY DIFFRACTIONr_gen_planes_other0.010.023037
X-RAY DIFFRACTIONr_nbd_refined0.2380.22725
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2140.210827
X-RAY DIFFRACTIONr_nbtor_refined0.1850.26204
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.26280
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2627
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0360.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1330.212
X-RAY DIFFRACTIONr_nbd_other0.2150.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1110.25
X-RAY DIFFRACTIONr_mcbond_it2.6222.8376233
X-RAY DIFFRACTIONr_mcbond_other2.6212.8386233
X-RAY DIFFRACTIONr_mcangle_it3.7025.0897779
X-RAY DIFFRACTIONr_mcangle_other3.7025.097780
X-RAY DIFFRACTIONr_scbond_it3.1823.0746417
X-RAY DIFFRACTIONr_scbond_other3.1813.0756418
X-RAY DIFFRACTIONr_scangle_it4.7515.5289515
X-RAY DIFFRACTIONr_scangle_other4.7515.5289516
X-RAY DIFFRACTIONr_lrange_it5.92927.06514366
X-RAY DIFFRACTIONr_lrange_other5.89727.04214314
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
2.13-2.1850.3053510.24964750.25269720.9410.95897.90590.225
2.185-2.2450.2943420.23962790.24267450.9440.96398.16160.213
2.245-2.310.2613520.21961420.22166130.9530.96998.20050.192
2.31-2.3810.2613250.20659920.20864240.9580.97398.33440.175
2.381-2.4590.2592780.19858440.20162240.9610.97698.36120.169
2.459-2.5450.2723090.19356240.19760260.9560.97798.45670.162
2.545-2.640.2552630.18954580.19258050.9620.97998.5530.158
2.64-2.7480.2852670.19452660.19856090.9540.97898.6450.162
2.748-2.870.2322690.18150440.18453910.9680.9898.55310.151
2.87-3.0090.2322870.1847780.18351360.9660.98198.61760.156
3.009-3.1710.2662350.18845760.19248870.9560.97998.44490.165
3.171-3.3630.242060.19343670.19646240.9670.97998.89710.173
3.363-3.5930.2332230.18840770.1943520.9680.98298.80510.172
3.593-3.8790.1852050.16738180.16840780.9790.98698.65130.155
3.879-4.2470.1781830.14335110.14537430.9820.98998.69090.136
4.247-4.7430.1741710.13431770.13633900.9830.9998.76110.13
4.743-5.4680.1721630.14428160.14529980.9860.9999.36620.138
5.468-6.6740.2061200.16624310.16825750.9790.98699.0680.159
6.674-9.3440.216950.16618750.16819900.9710.98598.9950.168
9.344-46.8180.172600.18511100.18411800.9830.98199.15250.212

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