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- PDB-3s5x: Structure of the cyanobacterial Oscillatoria Agardhii Agglutinin ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3s5x | |||||||||
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Title | Structure of the cyanobacterial Oscillatoria Agardhii Agglutinin (OAA) in complex with a3,a6 mannopentaose | |||||||||
![]() | Lectin | |||||||||
![]() | PROTEIN BINDING / BETA BARREL LIKE PROTEIN / ANTI-HIV LECTIN / CARBOHYDRATE | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Koharudin, L.M.I. / Gronenborn, A.M. | |||||||||
![]() | ![]() Title: Structural basis of the anti-HIV activity of the cyanobacterial Oscillatoria Agardhii agglutinin. Authors: Koharudin, L.M. / Gronenborn, A.M. #1: ![]() Title: Novel fold and carbohydrate specificity of the potent anti-HIV cyanobacterial lectin from Oscillatoria agardhii. Authors: Koharudin, L.M. / Furey, W. / Gronenborn, A.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 46.3 KB | Display | ![]() |
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PDB format | ![]() | 31.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 9.9 KB | Display | |
Data in CIF | ![]() | 13.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3s5vSC ![]() 3s60C 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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Unit cell |
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Components
#1: Protein | Mass: 14061.952 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 2.0 M (NH4)SO4 and 0.1 M Tris-HCl (pH 8.5) with protein and 3,6-mannopentaose at molar ratios of 1:2, 1:3, or 1:4 (the protein concentration kept at 40 mg/ml), VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 1, 2010 |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→35.19 Å / Num. all: 13024 / Num. obs: 13024 / % possible obs: 96.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2 / Redundancy: 12.02 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 27.5 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 8.91 % / Rmerge(I) obs: 0.118 / Mean I/σ(I) obs: 13.2 / % possible all: 87.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3S5V Resolution: 1.65→35.19 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.847 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.117 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.374 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→35.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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