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- PDB-9w4f: Crystal structure of beta-glucosidase CaBGL mutant E163Q in compl... -

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Basic information

Entry
Database: PDB / ID: 9w4f
TitleCrystal structure of beta-glucosidase CaBGL mutant E163Q in complex with glucose
Componentsbeta-glucosidase
KeywordsHYDROLASE / CaBGL / cellulose saccharification / Caldicellulosiruptor sp. F32
Function / homology
Function and homology information


beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / cytosol
Similarity search - Function
Glycoside hydrolase, family 1, beta-glucosidase / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
beta-D-glucopyranose / beta-glucosidase
Similarity search - Component
Biological speciesCaldicellulosiruptor sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsYou, C. / Feng, Y.G.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32200030 China
National Natural Science Foundation of China (NSFC)32170051 China
CitationJournal: Bioresour Technol / Year: 2025
Title: Engineering of beta-glucosidase CaBGL with improved performance in cellulose hydrolysis.
Authors: You, C. / Zheng, X. / Qi, K. / Dong, S. / Liu, Y.J. / Chen, C. / Cui, Q. / Feng, Y.
History
DepositionJul 31, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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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
E: beta-glucosidase
F: beta-glucosidase
G: beta-glucosidase
H: beta-glucosidase
I: beta-glucosidase
J: beta-glucosidase
K: beta-glucosidase
L: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)648,24061
Polymers642,75112
Non-polymers5,48849
Water17,294960
1
A: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0275
Polymers53,5631
Non-polymers4644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1196
Polymers53,5631
Non-polymers5565
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0275
Polymers53,5631
Non-polymers4644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0275
Polymers53,5631
Non-polymers4644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0275
Polymers53,5631
Non-polymers4644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0275
Polymers53,5631
Non-polymers4644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0275
Polymers53,5631
Non-polymers4644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0275
Polymers53,5631
Non-polymers4644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0275
Polymers53,5631
Non-polymers4644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0275
Polymers53,5631
Non-polymers4644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9395
Polymers53,5631
Non-polymers3764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9395
Polymers53,5631
Non-polymers3764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.030, 221.580, 236.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
beta-glucosidase / beta-glucosidase CaBGL


Mass: 53562.586 Da / Num. of mol.: 12 / Mutation: E163Q
Source method: isolated from a genetically manipulated source
Details: The sequence of organism Caldicellulosiruptor sp. is not available during the biocuration, replaced by I7DLX2 temporarily.
Source: (gene. exp.) Caldicellulosiruptor sp. (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: I7DLX2, beta-glucosidase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#3: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 10 / 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
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 960 / Source method: isolated from a natural source / Formula: H2O
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: 2.84 Å3/Da / Density % sol: 56.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 0.1M Bis-Tris, pH 6.5, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.26→36.92 Å / Num. obs: 339559 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.03 / Rrim(I) all: 0.077 / Χ2: 0.96 / Net I/σ(I): 17.7
Reflection shellResolution: 2.26→2.32 Å / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.607 / Num. measured all: 163276 / Num. unique obs: 24959 / CC1/2: 0.881 / Rpim(I) all: 0.257 / Rrim(I) all: 0.66 / Χ2: 0.87 / Net I/σ(I) obs: 3.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
xia2data reduction
PDB_EXTRACTdata extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→36.9 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.199 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2233 17163 5.1 %RANDOM
Rwork0.20266 ---
obs0.20371 322272 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.911 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2---1.66 Å20 Å2
3---2.21 Å2
Refinement stepCycle: 1 / Resolution: 2.26→36.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms45436 0 330 960 46726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01247071
X-RAY DIFFRACTIONr_bond_other_d0.0020.01643083
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.81163808
X-RAY DIFFRACTIONr_angle_other_deg0.5051.76799043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.71455422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.2265204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.002107888
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.070.26543
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0255566
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0211758
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.2924.48821724
X-RAY DIFFRACTIONr_mcbond_other4.2914.48821724
X-RAY DIFFRACTIONr_mcangle_it5.8398.04327134
X-RAY DIFFRACTIONr_mcangle_other5.8398.04327135
X-RAY DIFFRACTIONr_scbond_it5.1324.97525347
X-RAY DIFFRACTIONr_scbond_other5.1284.97425340
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.6588.88836663
X-RAY DIFFRACTIONr_long_range_B_refined9.80255.07218617
X-RAY DIFFRACTIONr_long_range_B_other9.80255.07218615
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.26→2.318 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 1275 -
Rwork0.274 23581 -
obs--99.99 %

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