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- PDB-5bvu: Crystal structure of Thermoanaerobacterium xylolyticum GH116 beta... -

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Basic information

Entry
Database: PDB / ID: 5bvu
TitleCrystal structure of Thermoanaerobacterium xylolyticum GH116 beta-glucosidase
Componentsbeta-glucosidase
KeywordsHYDROLASE / Thermoanaerobacterium xylolyticum / GH116 / beta-glucosidase / Glycoside Hydrolase
Function / homology
Function and homology information


glucosylceramidase / glucosylceramide catabolic process / glucosylceramidase activity / carbohydrate metabolic process / membrane / metal ion binding
Similarity search - Function
Glycosyl-hydrolase family 116, catalytic region / Beta-glucosidase GBA2-type / Glycosyl-hydrolase family 116, N-terminal / Glycosyl-hydrolase family 116, catalytic region / beta-glucosidase 2, glycosyl-hydrolase family 116 N-term / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Biological speciesThermoanaerobacterium xylanolyticum LX-11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.61 Å
AuthorsCharoenwattanasatien, R. / Pengthaisong, S. / Sansenya, S. / Mutoh, R. / Tanaka, H. / Kurisu, G. / Ketudat Cairns, J.R.
Funding support Thailand, Japan, 3items
OrganizationGrant numberCountry
The Thailand Research FundBRG5680012 Thailand
Suranaree University of Technology, National Research University Project of the Commission on Higher Education of Thailand Thailand
Institute for Protein Research, Osaka University Japan
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Bacterial beta-Glucosidase Reveals the Structural and Functional Basis of Genetic Defects in Human Glucocerebrosidase 2 (GBA2).
Authors: Charoenwattanasatien, R. / Pengthaisong, S. / Breen, I. / Mutoh, R. / Sansenya, S. / Hua, Y. / Tankrathok, A. / Wu, L. / Songsiriritthigul, C. / Tanaka, H. / Williams, S.J. / Davies, G.J. / ...Authors: Charoenwattanasatien, R. / Pengthaisong, S. / Breen, I. / Mutoh, R. / Sansenya, S. / Hua, Y. / Tankrathok, A. / Wu, L. / Songsiriritthigul, C. / Tanaka, H. / Williams, S.J. / Davies, G.J. / Kurisu, G. / Ketudat Cairns, J.R.
History
DepositionJun 5, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,37019
Polymers91,7941
Non-polymers1,57618
Water10,503583
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-13 kcal/mol
Surface area25670 Å2
Unit cell
Length a, b, c (Å)177.683, 54.271, 83.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein beta-glucosidase /


Mass: 91794.180 Da / Num. of mol.: 1 / Fragment: UNP residues 19-806
Source method: isolated from a genetically manipulated source
Details: The author believe that the E.C. number and the enzyme name in UniProt F6BL85 is incorrect.
Source: (gene. exp.) Thermoanaerobacterium xylanolyticum LX-11 (bacteria)
Strain: LX-11 / Gene: Thexy_2211 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: F6BL85, beta-glucosidase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 583 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.2 M Ammonium Sulfate, 23% PEG 3000, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.61→50 Å / Num. obs: 102998 / % possible obs: 99 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 34.4
Reflection shellResolution: 1.61→1.64 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 5.9 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.61→50 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.393 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17532 5069 4.9 %RANDOM
Rwork0.15378 ---
obs0.15482 97906 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.175 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0 Å2
2--0.01 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.61→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6221 0 101 583 6905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.026554
X-RAY DIFFRACTIONr_bond_other_d0.0010.025995
X-RAY DIFFRACTIONr_angle_refined_deg1.2941.9418862
X-RAY DIFFRACTIONr_angle_other_deg0.773313858
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3185783
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.13425.365315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.088151095
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0211512
X-RAY DIFFRACTIONr_chiral_restr0.080.2899
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027426
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021542
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_it1.0771.833105
X-RAY DIFFRACTIONr_mcbond_other1.0741.833104
X-RAY DIFFRACTIONr_mcangle_it1.7642.7443888
X-RAY DIFFRACTIONr_mcangle_other1.7642.7443889
X-RAY DIFFRACTIONr_scbond_it1.5032.0263449
X-RAY DIFFRACTIONr_scbond_other1.5032.0263449
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4032.9394972
X-RAY DIFFRACTIONr_long_range_B_refined4.62515.8688351
X-RAY DIFFRACTIONr_long_range_B_other4.43915.4218106
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.612→1.653 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 343 -
Rwork0.218 6533 -
obs--89.74 %

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