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- PDB-3hnu: 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: 3hnu | ||||||
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Title | Crystal structure of a designed Cyanovirin-N homolog lectin; LKAMG in P21 space group | ||||||
![]() | Cyanovirin-N-like protein | ||||||
![]() | SUGAR BINDING PROTEIN / Cyanovirin-N / CVNH / lectin | ||||||
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. / 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 | ![]() | 38.7 KB | Display | ![]() |
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PDB format | ![]() | 25.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 415.1 KB | Display | ![]() |
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Full document | ![]() | 415.1 KB | Display | |
Data in XML | ![]() | 7.9 KB | Display | |
Data in CIF | ![]() | 11 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hnxC ![]() 3hp8C ![]() 1m5m 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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Unit cell |
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Components
#1: Protein | Mass: 12386.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pET15b / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.65 % |
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Crystal grow | Temperature: 277 K / pH: 8 Details: 40 mg/ml protein in 0.2 M Li2SO4, 0.1 M Tris-HCl (pH 8.5), and 30% PEG 4000 at 8 to 1 ratio between protein and mother liquor, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 16, 2006 / Details: MIRRORS |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→24.49 Å / Num. obs: 14212 / % possible obs: 95.5 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 1.56→1.62 Å / Redundancy: 2.21 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 3.2 / % possible all: 71.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PSEUDO-MONOMERIC CV-N (1M5M) ![]() 1m5m Resolution: 1.56→24.49 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.542 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.105 / 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: 17.88 Å2
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Refinement step | Cycle: LAST / Resolution: 1.56→24.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.56→1.6 Å / Total num. of bins used: 20
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