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- PDB-3hp8: Crystal structure of a designed Cyanovirin-N homolog lectin; LKAM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3hp8 | |||||||||
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Title | Crystal structure of a designed Cyanovirin-N homolog lectin; LKAMG, bound to sucrose | |||||||||
![]() | Cyanovirin-N-like protein | |||||||||
![]() | SUGAR BINDING PROTEIN / Cyanovirin-N / CVNH / lectin / carbohydrate / sucrose | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Koharudin, L.M.I. / Furey, W. / Gronenborn, A.M. | |||||||||
![]() | ![]() Title: A designed chimeric cyanovirin-N homolog lectin: Structure and molecular basis of sucrose binding. Authors: Koharudin, L.M. / Furey, W. / Gronenborn, A.M. #1: ![]() Title: The Evolutionarily Conserved Family of Cyanovirin-N Homologs: Structures and Carbohydrate Specificity Authors: Koharudin, L.M.I. / Viscomi, A.R. / Jee, J.G. / Ottonello, S. / 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 | ![]() | 65.8 KB | Display | ![]() |
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PDB format | ![]() | 47.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 20.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hnuSC ![]() 3hnxC 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 12386.461 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pET15B / Production host: ![]() ![]() #2: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.18 % |
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Crystal grow | Temperature: 277 K / pH: 8 Details: protein solutions (~40 mg/ml) were incubated overnight with sucrose at a molar ratio of 1:40 (protein:disaccharide) and crystallization were carried out using 0.2 M Li2SO4, 0.1 M Tris-HCl ...Details: protein solutions (~40 mg/ml) were incubated overnight with sucrose at a molar ratio of 1:40 (protein:disaccharide) and crystallization were carried out using 0.2 M Li2SO4, 0.1 M Tris-HCl (pH 8.5), and 30% PEG 4000 with protein to mother liquor ratio of 8 to 1 , VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 10, 2007 |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→35.7 Å / Num. obs: 23572 / % possible obs: 96.7 % / Observed criterion σ(I): 3 / Redundancy: 3.08 % / Rmerge(I) obs: 0.166 / Net I/σ(I): 3.9 |
Reflection shell | Resolution: 1.88→1.95 Å / Redundancy: 2.92 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 1.4 / % possible all: 76.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3HNU Resolution: 2→35.7 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.905 / SU B: 4.761 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.187 / 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: 30.47 Å2
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Refinement step | Cycle: LAST / Resolution: 2→35.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
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