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- PDB-9iqb: Crystal structure of beta-glucosidase from Acetivibrio thermocellus -

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Basic information

Entry
Database: PDB / ID: 9iqb
TitleCrystal structure of beta-glucosidase from Acetivibrio thermocellus
ComponentsBeta-glucosidase A
KeywordsHYDROLASE / Beta-glucosidase / GH1 family / Cellobiose
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
Biological speciesAcetivibrio thermocellus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKamale, C. / Bhaumik, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR41982/PBD/26/822/2021 India
CitationJournal: Febs J. / Year: 2025
Title: Rational design facilitates the improvement of glucose tolerance and catalytic properties of a beta-glucosidase from Acetivibrio thermocellus.
Authors: Kamale, C. / Rauniyar, A. / Bhaumik, P.
History
DepositionJul 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-glucosidase A
B: Beta-glucosidase A
C: Beta-glucosidase A
D: Beta-glucosidase A
E: Beta-glucosidase A
F: Beta-glucosidase A
G: Beta-glucosidase A
H: Beta-glucosidase A
I: Beta-glucosidase A
J: Beta-glucosidase A
K: Beta-glucosidase A
L: Beta-glucosidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)631,66414
Polymers631,41912
Non-polymers2442
Water5,441302
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.930, 158.620, 158.910
Angle α, β, γ (deg.)60.118, 88.192, 87.478
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Beta-glucosidase A / Beta-D-glucoside glucohydrolase / Cellobiase / Gentiobiase


Mass: 52618.270 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio thermocellus (bacteria) / Gene: bglA, Cthe_0212 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P26208, beta-glucosidase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 3.86 Å3/Da / Density % sol: 68.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES, 55% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 3→35 Å / Num. obs: 175099 / % possible obs: 93.9 % / Redundancy: 1.99 % / CC1/2: 0.97 / Rmerge(I) obs: 0.165 / Rrim(I) all: 0.233 / Net I/σ(I): 4.33
Reflection shellResolution: 3→3.2 Å / Rmerge(I) obs: 0.65 / Num. unique obs: 31024 / CC1/2: 0.5 / Rrim(I) all: 0.92

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→34.991 Å / Cor.coef. Fo:Fc: 0.776 / Cor.coef. Fo:Fc free: 0.734 / SU B: 35.553 / SU ML: 0.6 / Cross valid method: FREE R-VALUE / ESU R Free: 0.576
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.35 8755 5 %
Rwork0.3 166344 -
all0.335 --
obs-175099 94.062 %
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: 39.256 Å2
Baniso -1Baniso -2Baniso -3
1-0.036 Å20.023 Å20.014 Å2
2---0.008 Å20.008 Å2
3----0.009 Å2
Refinement stepCycle: LAST / Resolution: 3→34.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms43908 0 16 303 44227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01345146
X-RAY DIFFRACTIONr_bond_other_d0.0050.01740928
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.63661098
X-RAY DIFFRACTIONr_angle_other_deg1.1421.5895216
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.46755376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.75623.3332412
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.489157740
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.40115180
X-RAY DIFFRACTIONr_chiral_restr0.0530.25616
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0250460
X-RAY DIFFRACTIONr_gen_planes_other0.0020.029840
X-RAY DIFFRACTIONr_nbd_refined0.230.211821
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2220.242694
X-RAY DIFFRACTIONr_nbtor_refined0.170.221355
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.218771
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.21284
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0850.229
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2410.257
X-RAY DIFFRACTIONr_nbd_other0.30.2116
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2210.214
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0790.21
X-RAY DIFFRACTIONr_mcbond_it2.1544.26721542
X-RAY DIFFRACTIONr_mcbond_other2.1534.26621541
X-RAY DIFFRACTIONr_mcangle_it3.6316.39426904
X-RAY DIFFRACTIONr_mcangle_other3.6316.39526905
X-RAY DIFFRACTIONr_scbond_it1.5544.18823604
X-RAY DIFFRACTIONr_scbond_other1.5534.18723601
X-RAY DIFFRACTIONr_scangle_it2.7576.29534194
X-RAY DIFFRACTIONr_scangle_other2.7566.29434193
X-RAY DIFFRACTIONr_lrange_it6.73749.06853369
X-RAY DIFFRACTIONr_lrange_other6.73849.07453366
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
3-3.0770.4156460.413122820.414136270.3680.59894.87050.412
3.077-3.1610.4146330.399120240.399133660.4440.69194.69550.394
3.161-3.2520.46160.383117030.384129850.5590.76894.8710.373
3.252-3.3510.4045930.368112760.37125490.6170.81394.58120.355
3.351-3.460.3765780.346109710.348122630.690.84494.17760.33
3.46-3.580.3735540.344105360.345118020.7280.85493.96710.329
3.58-3.7140.3735360.334101810.336114160.7220.86193.8770.318
3.714-3.8640.355160.32497950.326109840.7910.88193.87290.309
3.864-4.0330.3644920.33293610.334105070.7670.88293.77560.319
4.033-4.2270.3394740.31690030.318101360.8150.89293.49840.301
4.227-4.4520.3584490.31185210.31495300.7950.89194.12380.299
4.452-4.7170.3224260.30780980.30890920.810.89293.75270.292
4.717-5.0370.3334020.31576330.31685430.8040.87994.05360.299
5.037-5.4310.3553750.32271260.32479500.8330.88894.35220.302
5.431-5.9350.3653460.3465850.34173460.7980.86394.35070.317
5.935-6.6120.3543150.3259790.32266690.8180.87594.3770.302
6.612-7.590.3392760.31552530.31658960.8330.86793.77540.302
7.59-9.1880.3222340.29844400.29950090.8650.87793.3120.3
9.188-12.5670.2851820.30734600.30639460.8650.89392.2960.322
12.567-34.9910.3381120.32321170.32324130.8480.88992.37460.35

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