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Yorodumi- PDB-2xn1: Structure of alpha-galactosidase from Lactobacillus acidophilus N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xn1 | |||||||||
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Title | Structure of alpha-galactosidase from Lactobacillus acidophilus NCFM with TRIS | |||||||||
Components | ALPHA-GALACTOSIDASE | |||||||||
Keywords | HYDROLASE / GLYCOSIDASE | |||||||||
Function / homology | Function and homology information response to raffinose / alpha-galactosidase / alpha-galactosidase activity / carbohydrate catabolic process / protein homotetramerization Similarity search - Function | |||||||||
Biological species | LACTOBACILLUS ACIDOPHILUS NCFM (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Fredslund, F. / Abou Hachem, M. / Larsen, R.J. / Sorensen, P.G. / Lo Leggio, L. / Svensson, B. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Crystal Structure of Alpha-Galactosidase from Lactobacillus Acidophilus Ncfm: Insight Into Tetramer Formation and Substrate Binding. Authors: Fredslund, F. / Abou Hachem, M. / Jonsgaard Larsen, R. / Gerd Sorensen, P. / Coutinho, P.M. / Lo Leggio, L. / Svensson, B. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -5-STRANDED BARREL THIS IS REPRESENTED BY A -4-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xn1.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2xn1.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 2xn1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xn1_validation.pdf.gz | 486.1 KB | Display | wwPDB validaton report |
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Full document | 2xn1_full_validation.pdf.gz | 503.3 KB | Display | |
Data in XML | 2xn1_validation.xml.gz | 115 KB | Display | |
Data in CIF | 2xn1_validation.cif.gz | 168.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xn/2xn1 ftp://data.pdbj.org/pub/pdb/validation_reports/xn/2xn1 | HTTPS FTP |
-Related structure data
Related structure data | 2xn0SC 2xn2C 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: 84587.977 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LACTOBACILLUS ACIDOPHILUS NCFM (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q7WWP9, UniProt: G1UB44*PLUS, alpha-galactosidase #2: Chemical | ChemComp-TRS / #3: Chemical | ChemComp-GOL / #4: 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: 3.07 Å3/Da / Density % sol: 60 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 8-12% PEG8000, 0.1M TRIS, 10% GLYCEROL, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03908 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 27, 2009 / Details: MIRRORS |
Radiation | Monochromator: BENT SI (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03908 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→22 Å / Num. obs: 181263 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 12.38 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XN0 Resolution: 2.3→21.983 Å / SU ML: 0.28 / σ(F): 1.99 / Phase error: 16.63 / Stereochemistry target values: ML / Details: RESIDUES 1-4 ARE DISORDERED.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.216 Å2 / ksol: 0.434 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.3→21.983 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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