[English] 日本語
![](img/lk-miru.gif)
- PDB-1scr: HIGH-RESOLUTION STRUCTURES OF SINGLE-METAL-SUBSTITUTED CONCANAVAL... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1scr | ||||||
---|---|---|---|---|---|---|---|
Title | HIGH-RESOLUTION STRUCTURES OF SINGLE-METAL-SUBSTITUTED CONCANAVALIN A: THE CO,CA-PROTEIN AT 1.6 ANGSTROMS AND THE NI,CA-PROTEIN AT 2.0 ANGSTROMS | ||||||
![]() | CONCANAVALIN A | ||||||
![]() | LECTIN(AGGLUTININ) | ||||||
Function / homology | ![]() regulation of defense response to virus / D-mannose binding / defense response / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Emmerich, C. / Helliwell, J.R. / Redshaw, M. / Naismith, J.H. / Harrop, S.J. / Raftery, J. / Kalb, A.J. / Yariv, J. / Dauter, Z. / Wilson, K.S. | ||||||
![]() | ![]() Title: High-resolution structures of single-metal-substituted concanavalin A: the Co,Ca-protein at 1.6 A and the Ni,Ca-protein at 2.0 A. Authors: Emmerich, C. / Helliwell, J.R. / Redshaw, M. / Naismith, J.H. / Harrop, S.J. / Raftery, J. / Kalb, A.J. / Yariv, J. / Dauter, Z. / Wilson, K.S. #1: ![]() Title: Non-Glycosylated Recombinant Pro-Concanavalin a is Active without Polypeptide Cleavage Authors: Min, W. / Dunn, A.J. / Jones #2: ![]() Title: The Refined Structure of Cadmium Substituted Concanavalin a at 2.0 Angstroms Resolution Authors: Naismith, J.H. / Habash, J. / Harrop, S.J. / Helliwell, J.R. / Hunter, W.N. / Wan, T.C.M. / Weisgerber, S. / Kalb(Gilboa), A.J. / Yariv, J. #3: ![]() Title: The Effect of Metal Ion Homogeneity on the Diffraction Limit of Orthorhombic I222 Crystals of Concanavalin A Authors: Kalb(Gilboa), A.J. / Yariv, J. / Helliwell, J.R. / Papiz, M.Z. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 60.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 44.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: ALA 207 - ASP 208 OMEGA = 0.43 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION | ||||||||
Components on special symmetry positions |
| ||||||||
Details | THERE IS ONE MONOMER (237 AMINO ACIDS) IN THE ASYMMETRIC UNIT. CONCANAVALIN A EXISTS AS A TETRAMER ALTHOUGH THE ASYMMETRIC UNIT CONTAINS A MONOMER. THE TETRAMER CAN BE GENERATED BY SYMMETRY OPERATORS. |
-
Components
#1: Protein | Mass: 25622.385 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
---|---|
#2: Chemical | ChemComp-NI / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Compound details | KALB ET AL. (1988) POSTULATED IN A SURVEY OF THE RESOLUTION LIMITS OF A VARIETY OF METAL ...KALB ET AL. (1988) POSTULATED |
Sequence details | THE SEQUENCE IS AS DERIVED FROM THE CDNA SEQUENCE OF MIN ET AL.,1992. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.72 % | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 6.5 / Method: microdialysis / Details: Greer, J., (1970) J. Mol. Biol, 48, 365. | ||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Reflection | *PLUS Highest resolution: 2 Å / Num. obs: 16435 / % possible obs: 97.4 % / Observed criterion σ(I): 1 / Num. measured all: 60304 / Rmerge(I) obs: 0.04 |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2→8 Å / σ(F): 1 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.159 / Rfactor Rwork: 0.159 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.8 |