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Open data
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Basic information
Entry | Database: PDB / ID: 6x7h | ||||||
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Title | Cyanovirin-N Mutation I34Y with Dimannose bound | ||||||
![]() | Cyanovirin-N | ||||||
![]() | ANTIVIRAL PROTEIN / Mannose binding protein Antiviral protein | ||||||
Function / homology | Cyanovirin-N / Cyanovirin-N superfamily / CVNH domain / CVNH / regulation of defense response to virus / carbohydrate binding / 2alpha-alpha-mannobiose / Cyanovirin-N![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fromme, R. / Sharma, P. / Ghirlanda, G. | ||||||
![]() | ![]() Title: Design of novel cyanovirin-N variants by modulation of binding dynamics through distal mutations. Authors: Kazan, I.C. / Sharma, P. / Rahman, M.I. / Bobkov, A. / Fromme, R. / Ghirlanda, G. / Ozkan, S.B. #1: ![]() Title: Conformational gating of dimannose binding to the antiviral protein cyanovirin revealed from the crystal structure at 1.35 A resolution. Authors: Fromme, R. / Katiliene, Z. / Fromme, P. / Ghirlanda, G. #2: ![]() Title: A monovalent mutant of cyanovirin-N provides insight into the role of multiple interactions with gp120 for antiviral activity. Authors: Fromme, R. / Katiliene, Z. / Giomarelli, B. / Bogani, F. / Mc Mahon, J. / Mori, T. / Fromme, P. / Ghirlanda, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135 KB | Display | ![]() |
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PDB format | ![]() | 107.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 19.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2rdkS 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: 11999.111 Da / Num. of mol.: 2 / Mutation: I34Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.23 % / Description: Needle, 200 by 50 um |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / Details: 2 M ammonium sulfate, 5% isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2018 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.25→15.43 Å / Num. obs: 52827 / % possible obs: 92.7 % / Redundancy: 3.5 % / CC1/2: 0.991 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.053 / Rrim(I) all: 0.098 / Net I/σ(I): 9.6 / Num. measured all: 185048 / Scaling rejects: 87 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2RDK Resolution: 1.25→15.43 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.07 Å2 / Biso mean: 17.9278 Å2 / Biso min: 8.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.25→15.43 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
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