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- PDB-4j4e: Structure of P51G Cyanovirin-N swapped trimer in the P212121 spac... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4j4e | ||||||
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Title | Structure of P51G Cyanovirin-N swapped trimer in the P212121 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 | ![]() | 126.4 KB | Display | ![]() |
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PDB format | ![]() | 101.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.6 KB | Display | ![]() |
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Full document | ![]() | 462.3 KB | Display | |
Data in XML | ![]() | 22.2 KB | Display | |
Data in CIF | ![]() | 30.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4j4cC ![]() 4j4dC ![]() 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.: 6 / 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: 2.61 Å3/Da / Density % sol: 52.84 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 26% w/v PEG8000, 0.1 M sodium cacodylate, pH 6.5, 0.2 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 15, 2011 / Details: HF VariMax |
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: 2.4→68.773 Å / Num. all: 27748 / Num. obs: 26277 / % possible obs: 94.7 % / Observed criterion σ(F): 3 / Redundancy: 10.17 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 9.89 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1857 / % possible all: 91.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3EZM Resolution: 2.4→68.773 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.568 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.5 / ESU R Free: 0.302 / 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: 62.933 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→68.773 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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