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- PDB-9gci: The crystal structure of beta-glucosidase from the thermophilic b... -

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Basic information

Entry
Database: PDB / ID: 9gci
TitleThe crystal structure of beta-glucosidase from the thermophilic bacterium Caldicellulosiruptor saccharolyticus determined at 1.47 A resolution
Componentsbeta-glucosidase
KeywordsHYDROLASE / Biocatalysis / beta-glucosidase / Caldicellulosiruptor saccharolyticus
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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / beta-glucosidase
Similarity search - Component
Biological speciesCaldicellulosiruptor saccharolyticus DSM 8903 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsChrysina, E.D. / Sotiropoulou, A.I.
Funding support Greece, European Union, 4items
OrganizationGrant numberCountry
Other governmentMIS 5000432 Greece
Other governmentMIS 5002550 Greece
European Commission653706European Union
European Commission871037European Union
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2024
Title: Structural studies of beta-glucosidase from the thermophilic bacterium Caldicellulosiruptor saccharolyticus.
Authors: Sotiropoulou, A.I. / Hatzinikolaou, D.G. / Chrysina, E.D.
History
DepositionAug 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,99220
Polymers108,2372
Non-polymers1,75518
Water14,934829
1
A: beta-glucosidase
hetero molecules

B: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,99220
Polymers108,2372
Non-polymers1,75518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
Unit cell
Length a, b, c (Å)68.443, 98.718, 80.493
Angle α, β, γ (deg.)90.000, 97.487, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein beta-glucosidase


Mass: 54118.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The actual sequence of the enzyme is deposited with Uniprotkb with entry code: A4XIG7_CALS8 (https://www.uniprot.org/uniprotkb/A4XIG7/entry) In the present structure, additional amino acids ...Details: The actual sequence of the enzyme is deposited with Uniprotkb with entry code: A4XIG7_CALS8 (https://www.uniprot.org/uniprotkb/A4XIG7/entry) In the present structure, additional amino acids were incorporated at the N-terminus of Bgl1 (chain A) that correspond to the translated sequence of the pET15b plasmid between the thrombin cleavage site and the gene insertion point (BamHI) (residues SHMLEDP).
Source: (gene. exp.) Caldicellulosiruptor saccharolyticus DSM 8903 (bacteria)
Gene: Csac_1089
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A4XIG7, beta-glucosidase

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Non-polymers , 7 types, 847 molecules

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


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 829 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.49 Å3/Da / Density % sol: 50.62 % / Description: Thin plates
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M magnesium chloride hexahydrate, 0.1M Bis-Tris, pH 5.5, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: May 11, 2019
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.47→67.86 Å / Num. obs: 173397 / % possible obs: 96.5 % / Redundancy: 2.5 % / Biso Wilson estimate: 9.9 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.06 / Rrim(I) all: 0.068 / Net I/σ(I): 8.6
Reflection shellResolution: 1.47→1.5 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 8680 / CC1/2: 0.668 / Rpim(I) all: 0.574 / Rrim(I) all: 0.627 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→55.442 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.173 / SU ML: 0.043 / Cross valid method: FREE R-VALUE / ESU R: 0.059 / ESU R Free: 0.06
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1735 8764 5.055 %
Rwork0.153 164604 -
all0.154 --
obs-173368 96.419 %
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: 13.622 Å2
Baniso -1Baniso -2Baniso -3
1--0.151 Å2-0 Å2-0.276 Å2
2--0.717 Å20 Å2
3----0.477 Å2
Refinement stepCycle: LAST / Resolution: 1.47→55.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7596 0 111 829 8536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0127924
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167335
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.6610696
X-RAY DIFFRACTIONr_angle_other_deg0.4561.58416889
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1465914
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.246534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.909101331
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.2610410
X-RAY DIFFRACTIONr_chiral_restr0.0690.21094
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029227
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021937
X-RAY DIFFRACTIONr_nbd_refined0.220.21545
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.26788
X-RAY DIFFRACTIONr_nbtor_refined0.1920.23883
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.23824
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2601
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2120.217
X-RAY DIFFRACTIONr_nbd_other0.1970.2101
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2170.235
X-RAY DIFFRACTIONr_mcbond_it0.9161.2483650
X-RAY DIFFRACTIONr_mcbond_other0.9151.2483650
X-RAY DIFFRACTIONr_mcangle_it1.4122.2414560
X-RAY DIFFRACTIONr_mcangle_other1.4122.2424561
X-RAY DIFFRACTIONr_scbond_it21.5234274
X-RAY DIFFRACTIONr_scbond_other21.5234275
X-RAY DIFFRACTIONr_scangle_it3.2122.6536134
X-RAY DIFFRACTIONr_scangle_other3.2122.6536135
X-RAY DIFFRACTIONr_lrange_it4.46415.559351
X-RAY DIFFRACTIONr_lrange_other4.27513.7099151
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
1.47-1.5080.2826780.261121990.262132050.9450.95397.51610.256
1.508-1.5490.2686180.246116470.247129310.9540.9694.84960.237
1.549-1.5940.2296010.218117120.219125970.9650.96897.74550.206
1.594-1.6430.2176110.201114060.202122110.970.97398.41130.186
1.643-1.6970.2115930.186109920.187118070.9710.97798.11980.169
1.697-1.7570.1935770.168106240.169114510.9770.98297.81680.151
1.757-1.8230.1775450.159100550.16110390.980.98496.02320.143
1.823-1.8970.1825270.14997370.151106480.9790.98696.39370.134
1.897-1.9820.1714870.14594090.146101580.9820.98797.42080.132
1.982-2.0780.1574690.13890590.13997980.9850.98997.24430.128
2.078-2.190.1564110.13986280.13992790.9860.98997.41350.131
2.19-2.3230.1644780.13379040.13587600.9830.9995.68490.128
2.323-2.4830.1573840.12575580.12682650.9860.99196.0920.122
2.483-2.6820.1563620.12970790.1377050.9840.9996.57370.126
2.682-2.9370.163320.13464590.13570880.9850.98995.80980.135
2.937-3.2820.1573080.14157830.14264270.9840.98894.7720.146
3.282-3.7880.1442660.13850730.13956950.9870.98893.74890.15
3.788-4.6340.1432360.12942260.1347950.9890.99193.05530.147
4.634-6.530.1961880.16832180.1737480.9830.98990.87510.188
6.53-55.4420.159930.17518350.17421290.9890.98790.55890.202

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