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- PDB-1bga: BETA-GLUCOSIDASE A FROM BACILLUS POLYMYXA -

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Basic information

Entry
Database: PDB / ID: 1bga
TitleBETA-GLUCOSIDASE A FROM BACILLUS POLYMYXA
ComponentsBETA-GLUCOSIDASE A
KeywordsGLYCOSIDASE / FAMILY 1 BETA-GLUCOSIDASE / GLYCOSYL HYDROLASE
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
Biological speciesPaenibacillus polymyxa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSanz-Aparicio, J. / Hermoso, J.A. / 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 Bgla 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
DepositionApr 4, 1997Processing site: BNL
Revision 1.0Apr 15, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name

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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


Theoretical massNumber of molelcules
Total (without water)206,2704
Polymers206,2704
Non-polymers00
Water27,7611541
1
A: BETA-GLUCOSIDASE A
B: BETA-GLUCOSIDASE A
C: BETA-GLUCOSIDASE A
D: BETA-GLUCOSIDASE A

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


Theoretical massNumber of molelcules
Total (without water)412,5408
Polymers412,5408
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)205.460, 205.460, 155.860
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(-0.003907, -0.999992, 0.000477), (0.999971, -0.003904, 0.006489), (-0.006487, 0.000502, 0.999979)100.8571, -0.4535, 0.2254
2given(-0.999873, 0.002548, -0.015757), (-0.002653, -0.999975, 0.006625), (-0.01574, 0.006666, 0.999854)101.6991, 100.0745, 0.2218
3given(-0.002523, 0.999869, -0.015986), (-0.999997, -0.002534, -0.000679), (-0.000719, 0.015984, 0.999872)1.2893, 100.8196, -0.9391

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Components

#1: Protein
BETA-GLUCOSIDASE A / BGA


Mass: 51567.488 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1541 / 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 growpH: 8.3
Details: PROTEIN WAS CRYSTALLIZED FROM 1.3 M NA/K PHOSPHATE, PH 8.3, 5 MICRO-L PROTEIN, 14 MG/ML, 5 MICRO-L RESERVOIR
Crystal grow
*PLUS
Method: co-crystallization
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.3 Mphosphate1drop
2inhibitor1drop

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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: 2.4→26.54 Å / Num. obs: 117344 / % possible obs: 97.3 % / Observed criterion σ(I): 4 / Redundancy: 4.7 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 8.3
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.3 / % possible all: 92.3
Reflection
*PLUS
Num. measured all: 584536 / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
% possible obs: 92.3 %

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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: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CBG

1cbg


Resolution: 2.4→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.27 -7 %RANDOM
Rwork0.2 ---
obs0.2 92319 78.7 %-
Displacement parametersBiso mean: 19.6 Å2
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14576 0 16 1441 16033
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_deg1.51
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.35
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
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.4→2.51 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3 -7 %
Rwork0.25 8408 -
obs--70 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAMCSDX.PROTOPHCSD.PRO
X-RAY DIFFRACTION2PARAM19.SOLAMTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2 / Rfactor Rwork: 0.2
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
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.35
LS refinement shell
*PLUS
Rfactor Rfree: 0.3

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