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- PDB-8kaq: Glycoside hydrolase family 1 beta-glucosidase (E318G mutant) from... -

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Basic information

Entry
Database: PDB / ID: 8kaq
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 / alpha-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: To Be Published
Title: Identification of beta-1,2-glucan-associated glycoside hydrolase family 1 beta-glucosidase from Streptomyces griseus
Authors: Kumakura, H. / Motouchi, S. / Nakai, H. / Nakajima, M.
History
DepositionAug 3, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 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: Putative beta-glucosidase
B: Putative beta-glucosidase
C: Putative beta-glucosidase
D: Putative beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,40724
Polymers182,7624
Non-polymers2,64520
Water9,530529
1
A: Putative beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6328
Polymers45,6911
Non-polymers9427
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2726
Polymers45,6911
Non-polymers5815
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5977
Polymers45,6911
Non-polymers9066
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9063
Polymers45,6911
Non-polymers2162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 , 2 types, 11 molecules

#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.: 8
Source method: isolated from a genetically manipulated source
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
#4: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 538 molecules

#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H14O4
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 529 / 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: 2.35 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% PEG3350

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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 S 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
REFMAC5.8.0415refinement
XDSdata reduction
ARP/wARPmodel building
MOLREPphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→46.824 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.196 / WRfactor Rwork: 0.162 / SU B: 5.639 / SU ML: 0.143 / Average fsc free: 0.9634 / Average fsc work: 0.9761 / Cross valid method: FREE R-VALUE / ESU R: 0.234 / ESU R Free: 0.185
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2233 4704 5.038 %
Rwork0.1833 88660 -
all0.185 --
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: 28.114 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20.004 Å2
2--0.218 Å20 Å2
3---0.399 Å2
Refinement stepCycle: LAST / Resolution: 2.13→46.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12145 0 163 529 12837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01212650
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611332
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.66517294
X-RAY DIFFRACTIONr_angle_other_deg0.4881.58526025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.77851553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.8315107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.307101767
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.87510605
X-RAY DIFFRACTIONr_chiral_restr0.0650.21882
X-RAY DIFFRACTIONr_chiral_restr_other0.0070.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215409
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023037
X-RAY DIFFRACTIONr_nbd_refined0.2320.22716
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.210807
X-RAY DIFFRACTIONr_nbtor_refined0.1840.26213
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.26334
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2605
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0330.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1450.210
X-RAY DIFFRACTIONr_nbd_other0.1950.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1360.25
X-RAY DIFFRACTIONr_mcbond_it2.1522.8316233
X-RAY DIFFRACTIONr_mcbond_other2.1512.8316233
X-RAY DIFFRACTIONr_mcangle_it3.1785.0797779
X-RAY DIFFRACTIONr_mcangle_other3.1785.0797780
X-RAY DIFFRACTIONr_scbond_it2.6113.0486417
X-RAY DIFFRACTIONr_scbond_other2.6113.0486418
X-RAY DIFFRACTIONr_scangle_it4.0825.499515
X-RAY DIFFRACTIONr_scangle_other4.0825.499516
X-RAY DIFFRACTIONr_lrange_it5.33726.72814337
X-RAY DIFFRACTIONr_lrange_other5.326.70514283
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
2.13-2.1850.2983510.25264750.25469720.9430.95697.90590.229
2.185-2.2450.2913420.24262790.24467450.9460.96298.16160.217
2.245-2.310.2593520.22261420.22466130.9540.96898.20050.196
2.31-2.3810.2593250.2159920.21264240.9590.97298.33440.18
2.381-2.4590.2562780.20258440.20562240.9610.97598.36120.173
2.459-2.5450.2673090.19656240.260260.9570.97698.45670.166
2.545-2.640.2512630.19154580.19458050.9630.97898.5530.16
2.64-2.7480.2772670.19752660.20156090.9550.97798.6450.165
2.748-2.870.2252690.18450440.18653910.970.9898.55310.153
2.87-3.0090.2292870.18447780.18751360.9670.9898.61760.16
3.009-3.1710.2612350.1945760.19448870.9580.97898.44490.168
3.171-3.3630.2292060.19543670.19746240.970.97998.89710.175
3.363-3.5930.2282230.1940770.19243520.9690.98198.80510.174
3.593-3.8790.1812050.16938180.1740780.980.98598.65130.157
3.879-4.2470.1741830.14535110.14737430.9830.98998.69090.138
4.247-4.7430.171710.13631770.13733900.9840.9998.76110.131
4.743-5.4680.1711630.14728160.14829980.9870.98999.36620.141
5.468-6.6740.21200.16724310.16925750.980.98699.0680.16
6.674-9.3440.21950.16518750.16719900.9730.98598.9950.167
9.344-46.8240.17600.18511100.18411800.9850.98199.15250.213

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