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

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Basic information

Entry
Database: PDB / ID: 9gcj
TitleThe crystal structure of beta-glucosidase from the thermophilic bacterium Caldicellulosiruptor saccharolyticus in complex with beta-D-glucose determined at 1.95 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
beta-D-glucopyranose / DI(HYDROXYETHYL)ETHER / beta-glucosidase
Similarity search - Component
Biological speciesCaldicellulosiruptor saccharolyticus DSM 8903 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsChrysina, E.D. / Sotiropoulou, A.I.
Funding supportEuropean Union, 4items
OrganizationGrant numberCountry
Other governmentMIS 5000432
Other governmentMIS 5002550
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)109,3298
Polymers108,3512
Non-polymers9786
Water7,242402
1
A: beta-glucosidase
hetero molecules

B: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,3298
Polymers108,3512
Non-polymers9786
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
Unit cell
Length a, b, c (Å)68.161, 98.307, 81.776
Angle α, β, γ (deg.)90.000, 97.632, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein beta-glucosidase


Mass: 54175.371 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, a total of five (5) ...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, a total of five (5) amino acids were modelled at the N-terminus of Bgl1:molA. These residues originate from the translated sequence of the pET15b plasmid section (eight (8) amino acids, GSHMLEDP) between the thrombin cleavage site and the BamH I site in the multicloning area of the plasmid.
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
#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.: 2 / 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 , 4 types, 406 molecules

#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN
Nonpolymer detailsAdditional portions of density have been observed in the structure that could not be attributed to ...Additional portions of density have been observed in the structure that could not be attributed to any of the known molecules that were present during sample preparation, crystallisation and X-ray data collection. Non-specific binding of polyethylene glycol molecules is observed but there was not sufficient density to include all of them in the structure. These molecules have not been correlated with the functional role of the enzyme.

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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: 2.52 Å3/Da / Density % sol: 51.18 % / Description: Thin plates
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Co-crystals: 0.2 M magnesium chloride hexahydrate, 0.1M Bis-Tris, pH 5.5, 25% (w/v) PEG 3350 in the presence of 0.6 mM lactose

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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: Jul 8, 2021
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.95→98.31 Å / Num. obs: 77506 / % possible obs: 99.6 % / Redundancy: 6.7 % / CC1/2: 0.974 / Rpim(I) all: 0.095 / Rrim(I) all: 0.137 / Net I/σ(I): 8.3
Reflection shellResolution: 1.95→1.99 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4600 / CC1/2: 0.653 / Rpim(I) all: 0.634 / Rrim(I) all: 1.655 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→62.615 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.161 / SU ML: 0.111 / Cross valid method: FREE R-VALUE / ESU R: 0.15 / ESU R Free: 0.136
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2072 3968 5.121 %
Rwork0.1713 73511 -
all0.173 --
obs-77479 99.508 %
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: 31.517 Å2
Baniso -1Baniso -2Baniso -3
1--1.368 Å20 Å2-2.456 Å2
2--2.266 Å20 Å2
3----0.231 Å2
Refinement stepCycle: LAST / Resolution: 1.95→62.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7588 0 64 402 8054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0127876
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167266
X-RAY DIFFRACTIONr_angle_refined_deg1.1971.6610658
X-RAY DIFFRACTIONr_angle_other_deg0.4081.58416735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3395911
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.035534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.115101331
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.53810408
X-RAY DIFFRACTIONr_chiral_restr0.0590.21096
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029201
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021931
X-RAY DIFFRACTIONr_nbd_refined0.2130.21613
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.26873
X-RAY DIFFRACTIONr_nbtor_refined0.1910.23885
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.23835
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2412
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1930.218
X-RAY DIFFRACTIONr_nbd_other0.2580.284
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1090.29
X-RAY DIFFRACTIONr_mcbond_it1.9163.0593644
X-RAY DIFFRACTIONr_mcbond_other1.9133.0593644
X-RAY DIFFRACTIONr_mcangle_it2.8195.4924552
X-RAY DIFFRACTIONr_mcangle_other2.8185.4924553
X-RAY DIFFRACTIONr_scbond_it3.073.4544232
X-RAY DIFFRACTIONr_scbond_other3.073.4554233
X-RAY DIFFRACTIONr_scangle_it4.9056.1686105
X-RAY DIFFRACTIONr_scangle_other4.9056.1686106
X-RAY DIFFRACTIONr_lrange_it6.11531.5679176
X-RAY DIFFRACTIONr_lrange_other6.09131.2239107
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
1.95-2.0010.3132960.28154330.28357390.9230.93299.82580.265
2.001-2.0550.2953030.25453000.25756070.9280.94699.92870.235
2.055-2.1150.2632620.22950980.23153630.9470.95799.94410.211
2.115-2.180.2232630.20150540.20253190.9620.96799.96240.18
2.18-2.2510.2442500.19948470.20151020.9590.96999.9020.178
2.251-2.330.2382520.18847010.19149570.9620.97599.91930.168
2.33-2.4180.2272470.17545270.17747860.9640.97899.74930.157
2.418-2.5170.2162150.17543750.17746030.9660.97999.71760.16
2.517-2.6280.2112370.16241620.16444160.9710.98399.6150.149
2.628-2.7560.2052080.16139760.16342220.9710.98499.10.151
2.756-2.9050.2022290.14537560.14840250.9720.98799.00620.138
2.905-3.0810.1971850.16135390.16237760.9750.98598.62290.155
3.081-3.2930.1971880.16433520.16635970.9790.98598.41530.161
3.293-3.5560.2011680.16931680.1733600.9760.98699.28570.172
3.556-3.8940.1751540.15128730.15230570.9850.98999.01860.158
3.894-4.3520.1621460.13726070.13927720.9840.9999.31460.153
4.352-5.0210.1851320.13623170.13924610.9850.99199.51240.162
5.021-6.140.21940.17820150.1821140.9850.98899.76350.203
6.14-8.6410.193920.17815210.17916200.980.98699.56790.205
8.641-62.6150.222470.1988900.1999410.980.98499.57490.334

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