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- PDB-1qvb: CRYSTAL STRUCTURE OF THE BETA-GLYCOSIDASE FROM THE HYPERTHERMOPHI... -

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Basic information

Entry
Database: PDB / ID: 1qvb
TitleCRYSTAL STRUCTURE OF THE BETA-GLYCOSIDASE FROM THE HYPERTHERMOPHILE THERMOSPHAERA AGGREGANS
ComponentsBETA-GLYCOSIDASE
KeywordsHYDROLASE / TIM-BARREL / THERMOSTABLE
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermosphaera aggregans (archaea)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsChi, Y.-I. / Martinez-Cruz, L.A. / Swanson, R.V. / Robertson, D.E. / Kim, S.-H.
CitationJournal: FEBS Lett. / Year: 1999
Title: Crystal structure of the beta-glycosidase from the hyperthermophile Thermosphaera aggregans: insights into its activity and thermostability.
Authors: Chi, Y.I. / Martinez-Cruz, L.A. / Jancarik, J. / Swanson, R.V. / Robertson, D.E. / Kim, S.H.
History
DepositionJul 7, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 14, 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

Downloads & links

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Assembly

Deposited unit
A: BETA-GLYCOSIDASE
B: BETA-GLYCOSIDASE


Theoretical massNumber of molelcules
Total (without water)111,0062
Polymers111,0062
Non-polymers00
Water7,909439
1
A: BETA-GLYCOSIDASE
B: BETA-GLYCOSIDASE

A: BETA-GLYCOSIDASE
B: BETA-GLYCOSIDASE


Theoretical massNumber of molelcules
Total (without water)222,0114
Polymers222,0114
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)117.509, 102.215, 95.776
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-GLYCOSIDASE


Mass: 55502.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosphaera aggregans (archaea) / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YGA8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: SODIUM FORMATE, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13 Msodium formate1reservoir
220 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 20, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 45790 / Num. obs: 45287 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Biso Wilson estimate: 35.2 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 12.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.198 / % possible all: 95.3
Reflection shell
*PLUS
% possible obs: 95.3 % / Redundancy: 4 % / Mean I/σ(I) obs: 4.5

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.4→20 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: ENGH & HUBER
Details: NON-CRYSTALLOGRAPHIC SYMMETRY RESTRICTION EXCEPT THE FINAL STAGE, BULK SOLVENT CORRECTION
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2268 -RANDOM
Rwork0.21 ---
all0.228 45287 --
obs0.217 42922 93.7 %-
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7856 0 0 439 8295
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.473
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg22.193
X-RAY DIFFRACTIONx_improper_angle_deg0.738

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