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- PDB-1bgg: GLUCOSIDASE A FROM BACILLUS POLYMYXA COMPLEXED WITH GLUCONATE -

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Basic information

Entry
Database: PDB / ID: 1bgg
TitleGLUCOSIDASE A FROM BACILLUS POLYMYXA COMPLEXED WITH GLUCONATE
ComponentsBETA-GLUCOSIDASE A
KeywordsFAMILY 1 BETA-GLUCOSIDASE COMPLEX / GLYCOSYL-HYDROLASE COMPLEX
Function / homology
Function and homology information


scopolin beta-glucosidase activity / beta-glucosidase activity / beta-glucosidase / cellulose catabolic process
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 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...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 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
D-gluconic acid / Beta-glucosidase A
Similarity search - Component
Biological speciesPaenibacillus polymyxa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 2.3 Å
AuthorsSanz-Aparicio, J. / Hermoso, J. / Martinez-Ripoll, M. / Polaina, J.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Crystal structure of beta-glucosidase A from Bacillus polymyxa: insights into the catalytic activity in family 1 glycosyl hydrolases.
Authors: Sanz-Aparicio, J. / Hermoso, J.A. / Martinez-Ripoll, M. / Lequerica, J.L. / Polaina, J.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of a Type I Beta-Glucosidase Encoded by the Bgia Gene of Bacillus Polymyxa
Authors: Sanz-Aparicio, J. / Romero, A. / Martinez-Ripoll, M. / Madarro, A. / Flors, A. / Polaina, J.
#2: Journal: J.Bacteriol. / Year: 1992
Title: Purification and Characterization of a Bacillus Polymyxa Beta-Glucosidase Expressed in Escherichia Coli
Authors: Painbeni, E. / Valles, S. / Polaina, J. / Flors, A.
History
DepositionMay 12, 1997Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_validate_close_contact / software / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name / _pdbx_validate_close_contact.auth_atom_id_2 / _software.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 2, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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-GLUCOSIDASE A
B: BETA-GLUCOSIDASE A
C: BETA-GLUCOSIDASE A
D: BETA-GLUCOSIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,3837
Polymers206,7954
Non-polymers5883
Water26,9141494
1
A: BETA-GLUCOSIDASE A
B: BETA-GLUCOSIDASE A
C: BETA-GLUCOSIDASE A
D: BETA-GLUCOSIDASE A
hetero molecules

A: BETA-GLUCOSIDASE A
B: BETA-GLUCOSIDASE A
C: BETA-GLUCOSIDASE A
D: BETA-GLUCOSIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)414,76614
Polymers413,5908
Non-polymers1,1776
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)205.850, 205.850, 155.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.003894, -0.999992, 0.000619), (0.999987, -0.003892, 0.003321), (-0.003319, 0.000632, 0.999994)100.8596, -0.2334, 0.0763
2given(-0.999922, 0.003197, -0.012054), (-0.00323, -0.999991, 0.002769), (-0.012045, 0.002808, 0.999924)101.4297, 100.3949, 0.2175
3given(-0.001264, 0.999915, -0.012957), (-0.999998, -0.001283, -0.001452), (-0.001468, 0.012955, 0.999915)1.0074, 100.8103, -0.791

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Components

#1: Protein
BETA-GLUCOSIDASE A / BGA


Mass: 51698.688 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus polymyxa (bacteria) / Gene: BGLA / Plasmid: PUC DERIVATIVE / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 (DE3) / References: UniProt: P22073, beta-glucosidase
#2: Sugar ChemComp-GCO / D-gluconic acid / GLUCONIC ACID / Gluconic acid


Type: D-saccharide / Mass: 196.155 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1494 / 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: 4.2 Å3/Da / Density % sol: 70 %
Crystal growMethod: co-crystallization / pH: 8.3
Details: COMPLEX WAS OBTAINED BY CO-CRYSTALLIZATION, 5 MICRO-L BGLA (14 MG/ML) / 5 MICRO-L 10MM LIGAND / 5 MICRO-L PP 1.3M, PH 8.3, co-crystallization
Crystal grow
*PLUS
Method: co-crystallization
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
21.3 Mphosphate1drop
1inhibitor1drop

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Data collection

DiffractionMean temperature: 176 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Type: LURE / Wavelength: 0.983
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.983 Å / Relative weight: 1
ReflectionResolution: 2.3→31.4 Å / Num. obs: 146539 / % possible obs: 99.4 % / Observed criterion σ(I): 4 / Redundancy: 5.7 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 6.2
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2 / Rsym value: 0.32 / % possible all: 97.2
Reflection
*PLUS
Num. measured all: 840221 / Rmerge(I) obs: 0.092
Reflection shell
*PLUS
% possible obs: 97.2 %

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Processing

Software
NameVersionClassification
X-PLOR3.843model building
X-PLOR3.843refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.843phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 1BGA

1bga


Resolution: 2.3→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.25 -7 %RANDOM
Rwork0.2 ---
obs0.2 107900 75.6 %-
Displacement parametersBiso mean: 14.4 Å2
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14576 0 55 1494 16125
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.56
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.01
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.38
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
LS refinement shellResolution: 2.3→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.29 -7 %
Rwork0.24 10518 -
obs--66 %
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 14576
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.01
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.38

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