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- PDB-1tr1: CRYSTAL STRUCTURE OF E96K MUTATED BETA-GLUCOSIDASE A FROM BACILLU... -

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Basic information

Entry
Database: PDB / ID: 1tr1
TitleCRYSTAL STRUCTURE OF E96K MUTATED BETA-GLUCOSIDASE A FROM BACILLUS POLYMYXA, AN ENZYME WITH INCREASED THERMORESISTANCE
ComponentsBETA-GLUCOSIDASE A
KeywordsFAMILY 1 BETA-GLUCOSIDASE / INCREASED THERMORESISTANCE
Function / homology
Function and homology information


: / beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / cytosol
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 / DIFFERENCE FOURIER / Resolution: 2.2 Å
AuthorsSanz-Aparicio, J. / Hermoso, J.A. / Martinez-Ripoll, M. / Gonzalez-Perez, B. / 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: Biochem.J. / Year: 1996
Title: Amino Acid Substitutions Enhancing Thermostability of Bacillus Polymyxa Beta-Glucosidase A
Authors: Lopez-Camacho, C. / Salgado, J. / Lequerica, J.L. / Madarro, A. / Ballestar, E. / Franco, L. / Polaina, J.
History
DepositionMar 12, 1998Processing site: BNL
Revision 1.0Apr 20, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Other / Category: pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.6Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)206,6398
Polymers206,2704
Non-polymers3684
Water27,6711536
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)413,27716
Polymers412,5408
Non-polymers7378
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)205.030, 205.030, 155.430
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(-0.003753, -0.999993, 0.000702), (0.999986, -0.00375, 0.003738), (-0.003735, 0.000717, 0.999993)100.4128, -0.02439, 0.1263
2given(-0.999927, 0.003134, -0.011634), (-0.003163, -0.999992, 0.002514), (-0.011626, 0.00255, 0.999929)100.9677, 99.9612, 0.2156
3given(-0.000497, 0.999925, -0.012226), (-0.999998, -0.000518, -0.001737), (-0.001743, 0.012225, 0.999924)0.959, 100.3355, -0.7361

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Components

#1: Protein
BETA-GLUCOSIDASE A / BGA


Mass: 51567.555 Da / Num. of mol.: 4 / Mutation: E96K
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): DHS-ALPHA / References: UniProt: P22073, beta-glucosidase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1536 / 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: pH 8.3
Crystal grow
*PLUS

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 1.0375
DetectorDetector: CCD / Date: Oct 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0375 Å / Relative weight: 1
ReflectionResolution: 2.2→32 Å / Num. obs: 164213 / % possible obs: 98.4 % / Observed criterion σ(I): 4 / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 12.7
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 2.8 / % possible all: 97.8

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Processing

Software
NameVersionClassification
X-PLOR3.843model building
X-PLOR3.843refinement
XDSdata reduction
XSCALAdata scaling
CCP4(TRUNCATE)data scaling
X-PLOR3.843phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: 1BGA

1bga


Resolution: 2.2→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.282 14925 7 %RANDOM
Rwork0.21 ---
obs0.21 157900 75.6 %-
Displacement parametersBiso mean: 14.4 Å2
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14576 0 24 1536 16136
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_it2.91.5
X-RAY DIFFRACTIONx_mcangle_it3.92
X-RAY DIFFRACTIONx_scbond_it2.91.5
X-RAY DIFFRACTIONx_scangle_it3.92
Refine LS restraints NCSNCS model details: NCS RESTRAINTS / Rms dev Biso : 1.82 Å2 / Weight Biso : 2
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.29 1412 7 %
Rwork0.24 10518 -
obs--66 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAMCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL

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