+Open data
-Basic information
Entry | Database: PDB / ID: 1bga | ||||||
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Title | BETA-GLUCOSIDASE A FROM BACILLUS POLYMYXA | ||||||
Components | BETA-GLUCOSIDASE A | ||||||
Keywords | GLYCOSIDASE / FAMILY 1 BETA-GLUCOSIDASE / GLYCOSYL HYDROLASE | ||||||
Function / homology | Function and homology information scopolin beta-glucosidase activity / beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / cytosol Similarity search - Function | ||||||
Biological species | Paenibacillus polymyxa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Sanz-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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bga.cif.gz | 391.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bga.ent.gz | 320.7 KB | Display | PDB format |
PDBx/mmJSON format | 1bga.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/1bga ftp://data.pdbj.org/pub/pdb/validation_reports/bg/1bga | HTTPS FTP |
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-Related structure data
Related structure data | 1bggC 1tr1C 1cbgS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.2 Å3/Da / Density % sol: 70 % | |||||||||||||||
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Crystal grow | pH: 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
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-Data collection
Diffraction | Mean temperature: 176 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Type: LURE / Wavelength: 0.983 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.983 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CBG Resolution: 2.4→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 19.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.51 Å / Total num. of bins used: 8
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Xplor file |
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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
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LS refinement shell | *PLUS Rfactor Rfree: 0.3 |