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- PDB-4xpq: Crystal structure of Pedobacter saltans GH31 alpha-galactosidase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4xpq | ||||||
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Title | Crystal structure of Pedobacter saltans GH31 alpha-galactosidase complexed with L-fucose | ||||||
![]() | Alpha-glucosidase | ||||||
![]() | HYDROLASE / TIM-barrel / GH31 | ||||||
Function / homology | ![]() hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Miyazaki, T. / Ishizaki, Y. / Ichikawa, M. / Nishikawa, A. / Tonozuka, T. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163.7 KB | Display | ![]() |
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PDB format | ![]() | 124.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.8 KB | Display | ![]() |
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Full document | ![]() | 469.7 KB | Display | |
Data in XML | ![]() | 30.3 KB | Display | |
Data in CIF | ![]() | 46.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xpoSC ![]() 4xppC ![]() 4xprC ![]() 4xpsC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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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.) ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-TRS / | ||||||
#3: Sugar | #4: Chemical | ChemComp-EDO / #5: 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% PEG MME 2000, 100 mM Tris-HCl, soaked with 500 mM L-fucose |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1.85→50 Å / Num. obs: 62800 / % possible obs: 100 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 31.7 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 4.9 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4XPO Resolution: 1.85→40.02 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.158 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.101 / 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: 20.741 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→40.02 Å
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Refine LS restraints |
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