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Yorodumi- PDB-4xpp: Crystal structure of Pedobacter saltans GH31 alpha-galactosidase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xpp | ||||||
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Title | Crystal structure of Pedobacter saltans GH31 alpha-galactosidase complexed with D-galactose | ||||||
Components | Alpha-glucosidase | ||||||
Keywords | HYDROLASE / TIM-barrel / GH31 | ||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Pedobacter saltans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Miyazaki, T. / Ishizaki, Y. / Ichikawa, M. / Nishikawa, A. / Tonozuka, T. | ||||||
Citation | Journal: Biochem.J. / Year: 2015 Title: Structural and biochemical characterization of novel bacterial alpha-galactosidases belonging to glycoside hydrolase family 31 Authors: Miyazaki, T. / Ishizaki, Y. / Ichikawa, M. / Nishikawa, A. / Tonozuka, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xpp.cif.gz | 151.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xpp.ent.gz | 115.5 KB | Display | PDB format |
PDBx/mmJSON format | 4xpp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xp/4xpp ftp://data.pdbj.org/pub/pdb/validation_reports/xp/4xpp | HTTPS FTP |
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-Related structure data
Related structure data | 4xpoSC 4xpqC 4xprC 4xpsC 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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-Components
#1: Protein | Mass: 81427.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pedobacter saltans (bacteria) / Strain: NBRC 100064 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0F7R6D6*PLUS, alpha-galactosidase | ||||
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#2: Sugar | ChemComp-GAL / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE IS BASED ON GENBANK BAR72452.1. N-TERMINAL RESIDUES MGSSHHHHHHSSGLVPRGSHMA REPRESENT ...THE SEQUENCE IS BASED ON GENBANK BAR72452.1. N-TERMINAL RESIDUES MGSSHHHHHH | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% PEG MME 2000, 100 mM HEPES-NaOH, 50 mM galactose PH range: 7.5 - 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 32895 / % possible obs: 99.9 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 32.5 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 5.9 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XPO Resolution: 2.3→39.52 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.662 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→39.52 Å
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