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- PDB-3obl: Crystal structure of the potent anti-HIV cyanobacterial lectin fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3obl | ||||||
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Title | Crystal structure of the potent anti-HIV cyanobacterial lectin from Oscillatoria Agardhii | ||||||
![]() | Lectin | ||||||
![]() | SUGAR BINDING PROTEIN / novel beta barrel fold / anti-HIV lectin / High mannose glycans | ||||||
Function / homology | Lipocalin - #450 / OAA-family lectin sugar binding domain / OAA-family lectin sugar binding domain / Lipocalin / carbohydrate binding / Beta Barrel / Mainly Beta / Lectin![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Koharudin, L.M.I. / Furey, W. / Gronenborn, A.M. | ||||||
![]() | ![]() 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. #1: Journal: J.Biol.Chem. / Year: 2007 Title: Primary structure and carbohydrate binding specificity of a potent anti-HIV lectin isolated from the filamentous cyanobacterium Oscillatoria agardhii Authors: Sato, Y. / Okuyama, S. / Hori, K. #2: ![]() Title: Cloning, expression, and characterization of a novel anti-HIV lectin from the cultured cyanobacterium, Oscillatoria agardhii Authors: Sato, T. / Hori, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 133.6 KB | Display | ![]() |
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PDB format | ![]() | 105.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.2 KB | Display | ![]() |
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Full document | ![]() | 451.7 KB | Display | |
Data in XML | ![]() | 16.7 KB | Display | |
Data in CIF | ![]() | 25 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Unit cell |
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Components
#1: Protein | Mass: 13930.758 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Expressed as native protein / Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CXS / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.54 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1.2 M NaH2PO4/0.8 M K2HPO4, 0.2 M Li2SO4, 0.1 M CAPS (pH 10.5), VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 277 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 25, 2010 / Details: MIRRORS | ||||||||||||
Radiation | Monochromator: ROSENBAUM-ROCK MONOCHROMATOR HIGH-RESOLUTION DOUBLE-CRYSTAL SI(220) SAGITTAL FOCUSING, ROSENBAUM- ROCK VERTICAL FOCUSING MIRROR Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.1→22.64 Å / Num. obs: 86175 / % possible obs: 92 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 3.81 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 7.5 | ||||||||||||
Reflection shell | Resolution: 1.1→1.14 Å / Redundancy: 3.73 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 2.1 / Num. unique all: 9892 / % possible all: 83.1 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE DATA HAVE BEEN COLLECTED UP 1.10 A RESOLUTION. HOWEVER, REFINEMENT CONVERGED TO BETTER R VALUES BY CUTTING THE RESOLUTION TO 1.20 A.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.854 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→22.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Total num. of bins used: 20
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