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- PDB-6ier: Apo structure of a beta-glucosidase 1317 -

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Basic information

Entry
Database: PDB / ID: 6ier
TitleApo structure of a beta-glucosidase 1317
Componentsbeta-glucosidase 1317
KeywordsHYDROLASE / beta-glucosidase / glucose tolerance / substrate specificity
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 hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Glycosidases / Glycoside hydrolase superfamily ...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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Beta-glucosidase 1317
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.246 Å
AuthorsXie, W. / Liu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31700657 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2019
Title: Improving the cellobiose-hydrolysis activity and glucose-tolerance of a thermostable beta-glucosidase through rational design.
Authors: Liu, X. / Cao, L. / Zeng, J. / Liu, Y. / Xie, W.
History
DepositionSep 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 1317
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9162
Polymers48,7941
Non-polymers1221
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint3 kcal/mol
Surface area15000 Å2
2
A: beta-glucosidase 1317
hetero molecules

A: beta-glucosidase 1317
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,8324
Polymers97,5882
Non-polymers2442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area2620 Å2
ΔGint-2 kcal/mol
Surface area28040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.990, 122.990, 48.760
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein beta-glucosidase 1317


Mass: 48793.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A5H1ZR35*PLUS
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.18 Å3/Da / Density % sol: 43.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris-HCl (pH 8.5), 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OXFORD DIFFRACTION NOVA / Wavelength: 1.54 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Sep 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.24→39.2 Å / Num. obs: 20173 / % possible obs: 99.1 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.1
Reflection shellResolution: 2.25→2.37 Å / Rmerge(I) obs: 0.293 / Num. unique obs: 2775 / CC1/2: 0.84 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
CrysalisProdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GNX

5gnx


Resolution: 2.246→30.747 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.13
RfactorNum. reflection% reflection
Rfree0.2362 993 4.93 %
Rwork0.2062 --
obs0.2076 20158 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.246→30.747 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3121 0 8 139 3268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043229
X-RAY DIFFRACTIONf_angle_d0.7014400
X-RAY DIFFRACTIONf_dihedral_angle_d15.2521883
X-RAY DIFFRACTIONf_chiral_restr0.046472
X-RAY DIFFRACTIONf_plane_restr0.006582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2461-2.36450.32281460.29512568X-RAY DIFFRACTION94
2.3645-2.51250.27161380.24542718X-RAY DIFFRACTION100
2.5125-2.70640.26931500.23532738X-RAY DIFFRACTION100
2.7064-2.97860.27381430.2322733X-RAY DIFFRACTION100
2.9786-3.40910.23381570.20912759X-RAY DIFFRACTION100
3.4091-4.29330.21431200.18082792X-RAY DIFFRACTION100
4.2933-30.75040.15631390.14382857X-RAY DIFFRACTION100

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