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- PDB-3hnx: 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: 3hnx | ||||||
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Title | Crystal structure of a designed Cyanovirin-N homolog lectin; LKAMG in P212121 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.I. / Viscomi, A. / Jee, J. / 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 | ![]() | 65.5 KB | Display | ![]() |
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PDB format | ![]() | 48.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.7 KB | Display | ![]() |
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Full document | ![]() | 426.7 KB | Display | |
Data in XML | ![]() | 8 KB | Display | |
Data in CIF | ![]() | 10.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hnuSC ![]() 3hp8C 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: 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: 2.14 Å3/Da / Density % sol: 42.46 % |
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Crystal grow | Temperature: 277 K / pH: 8 Details: 50 mg/ml protein concentration in 0.2 M Li2SO4, 0.1 M Tris-HCl (pH 8.5), and 30% PEG 4000 at 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 SATURN 944 / Detector: CCD / Date: Oct 17, 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: 1.35→27.26 Å / Num. obs: 23394 / % possible obs: 97.7 % / Observed criterion σ(I): 3 / Redundancy: 13.32 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 40.7 |
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 2.94 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 2.7 / % possible all: 77.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3HNU Resolution: 1.37→27.26 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.643 / SU ML: 0.031 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.066 / 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: 18.02 Å2
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Refinement step | Cycle: LAST / Resolution: 1.37→27.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.37→1.41 Å / Total num. of bins used: 20
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