+Open data
-Basic information
Entry | Database: PDB / ID: 1jyi | ||||||
---|---|---|---|---|---|---|---|
Title | CONCANAVALIN A/12-MER PEPTIDE COMPLEX | ||||||
Components |
| ||||||
Keywords | SUGAR BINDING PROTEIN / LECTIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Canavalia ensiformis (jack bean) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.75 Å | ||||||
Authors | Jain, D. / Kaur, K.J. / Sundaravadivel, B. / Salunke, D.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: Structural and Functional Consequences of Peptide-carbohydrate Mimicry. Crystal Structure of a Carbohydrate-mimicking Peptide Bound to Concanavalin A. Authors: Jain, D. / Kaur, K.J. / Sundaravadivel, B. / Salunke, D.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1jyi.cif.gz | 189.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1jyi.ent.gz | 154.3 KB | Display | PDB format |
PDBx/mmJSON format | 1jyi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/1jyi ftp://data.pdbj.org/pub/pdb/validation_reports/jy/1jyi | HTTPS FTP |
---|
-Related structure data
Related structure data | 5cnaS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 25622.385 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P55915 #2: Protein/peptide | Mass: 1365.444 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3.55 Å3/Da / Density % sol: 65.32 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 9 / Method: vapor diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å |
---|---|
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→10 Å / Num. obs: 34767 / % possible obs: 86.4 % / Redundancy: 3 % / Rmerge(I) obs: 0.67 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.75→10 Å |
Reflection | *PLUS Redundancy: 3 % / Num. measured all: 47255 / Rmerge(I) obs: 0.067 |
Reflection shell | *PLUS Lowest resolution: 3.07 Å / % possible obs: 67.5 % |
-Processing
Software |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Starting model: 5CNA Resolution: 2.75→10 Å / σ(F): 0 /
| |||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→10 Å
| |||||||||||||||
Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.192 | |||||||||||||||
Solvent computation | *PLUS | |||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||
Refine LS restraints | *PLUS
|