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Yorodumi- PDB-4j4g: Structure of P51G Cyanovirin-N swapped tetramer in the C2 space group -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j4g | ||||||
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Title | Structure of P51G Cyanovirin-N swapped tetramer in the C2 space group | ||||||
Components | Cyanovirin-N | ||||||
Keywords | SUGAR BINDING PROTEIN / CVNH fold / carbohydrate binding protein / antiviral protein | ||||||
Function / homology | Cyanovirin-N / Cyanovirin-N superfamily / CVNH domain / CVNH / regulation of defense response to virus / carbohydrate binding / Cyanovirin-N Function and homology information | ||||||
Biological species | Nostoc ellipsosporum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.92 Å | ||||||
Authors | Koharudin, L.M.I. / Liu, L. / Gronenborn, A.M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j4g.cif.gz | 95.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j4g.ent.gz | 75.3 KB | Display | PDB format |
PDBx/mmJSON format | 4j4g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4j4g_validation.pdf.gz | 426.9 KB | Display | wwPDB validaton report |
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Full document | 4j4g_full_validation.pdf.gz | 427.5 KB | Display | |
Data in XML | 4j4g_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | 4j4g_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/4j4g ftp://data.pdbj.org/pub/pdb/validation_reports/j4/4j4g | HTTPS FTP |
-Related structure data
Related structure data | 4j4cC 4j4dC 4j4eC 4j4fC 3ezmS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Nostoc ellipsosporum (bacteria) / Plasmid: pET26B / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: P81180 #2: Water | ChemComp-HOH / | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.75 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.8 M potassium phosphate dibasic, 1.2 M sodium phosphate monobasic, 0.1 M CAPS, pH 10.5, 0.2 M lithium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 28, 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: 1.92→29.4 Å / Num. all: 40946 / Num. obs: 40086 / % possible obs: 97.9 % / Observed criterion σ(F): 3 / Redundancy: 5.68 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.92→1.99 Å / Redundancy: 3.07 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2643 / % possible all: 89.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EZM Resolution: 1.92→29.4 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.203 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.161 / ESU R Free: 0.15 / 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: 30.363 Å2
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Refinement step | Cycle: LAST / Resolution: 1.92→29.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.92→1.97 Å / Total num. of bins used: 20
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