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- PDB-5swb: Crystal structure of N-glycan transport solute binding protein (N... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5swb | |||||||||
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Title | Crystal structure of N-glycan transport solute binding protein (NgtS) from Streptococcus pneumoniae in complex with Man5GlcNAc | |||||||||
![]() | Extracellular solute-binding protein | |||||||||
![]() | HYDROLASE / Solute binding protein / protein-glycan complex / alpha/beta domain | |||||||||
Function / homology | : / : ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Robb, M. / Boraston, A.B. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular Characterization of N-glycan Degradation and Transport in Streptococcus pneumoniae and Its Contribution to Virulence. Authors: Robb, M. / Hobbs, J.K. / Woodiga, S.A. / Shapiro-Ward, S. / Suits, M.D. / McGregor, N. / Brumer, H. / Yesilkaya, H. / King, S.J. / Boraston, A.B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 420.7 KB | Display | ![]() |
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PDB format | ![]() | 339.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5suoSC ![]() 5swaC ![]() 5swiC C: citing same article ( S: Starting model for refinement |
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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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 53292.781 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-5)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-5)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Type: oligosaccharide / Mass: 1031.912 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source #4: Chemical | ChemComp-CD / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.41 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 30 % PEG 400, 0.1 M cadmium chloride hydrate, 0.1 M sodium acetate trihydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 11, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98005 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→99.76 Å / Num. obs: 234916 / % possible obs: 99.9 % / Redundancy: 4.7 % / Net I/σ(I): 25.4 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 5SUO Resolution: 1.73→99.76 Å / SU B: 2.549 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.106 / Details: U VALUES : REFINED INDIVIDUALLY
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Displacement parameters | Biso mean: 29.96 Å2
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Refinement step | Cycle: LAST / Resolution: 1.73→99.76 Å
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