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- PDB-4j4d: Structure of P51G Cyanovirin-N swapped dimer in the P21212 space group -
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Open data
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Basic information
Entry | Database: PDB / ID: 4j4d | ||||||
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Title | Structure of P51G Cyanovirin-N swapped dimer in the P21212 space group | ||||||
![]() | Cyanovirin-N | ||||||
![]() | SUGAR BINDING PROTEIN / CVNH fold / carbohydrate binding protein / antiviral protein | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Koharudin, L.M.I. / Liu, L. / Gronenborn, A.M. | ||||||
![]() | ![]() Title: Different 3D domain-swapped oligomeric cyanovirin-N structures suggest trapped folding intermediates. Authors: Koharudin, L.M. / Liu, L. / 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 | ![]() | 92.6 KB | Display | ![]() |
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PDB format | ![]() | 72.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.5 KB | Display | ![]() |
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Full document | ![]() | 441.3 KB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 25.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4j4cC ![]() 4j4eC ![]() 4j4fC ![]() 4j4gC ![]() 3ezmS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10982.026 Da / Num. of mol.: 4 / Mutation: P51G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.54 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 40% ethanol, 0.1 M sodium phosphate/citrate, pH 4.2, 5% w/v PEG1000, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 10, 2011 / Details: MIRRORS |
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: 1.89→52.31 Å / Num. all: 30944 / Num. obs: 28499 / % possible obs: 92.1 % / Observed criterion σ(F): 3 / Redundancy: 8.75 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.89→1.96 Å / Redundancy: 8.18 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1718 / % possible all: 86.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3EZM Resolution: 2→52.31 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.716 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.255 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 53.215 Å2
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Refinement step | Cycle: LAST / Resolution: 2→52.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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