[English] 日本語
![](img/lk-miru.gif)
- PDB-1c57: DIRECT DETERMINATION OF THE POSITIONS OF DEUTERIUM ATOMS OF BOUND... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1c57 | ||||||
---|---|---|---|---|---|---|---|
Title | DIRECT DETERMINATION OF THE POSITIONS OF DEUTERIUM ATOMS OF BOUND WATER IN CONCANAVALIN A BY NEUTRON LAUE CRYSTALLOGRAPHY | ||||||
![]() | Concanavalin-Br | ||||||
![]() | SUGAR BINDING PROTEIN / CONCANAVALIN A / NEUTRON LAUE DIFFRACTION / BOUND D2O MOLECULES | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | NEUTRON DIFFRACTION / NUCLEAR REACTOR / Resolution: 2.4 Å | ||||||
![]() | Habash, J. / Raftery, J. / Nuttall, R. / Price, H.J. / Lehmann, M.S. / Wilkinson, C. / Kalb, A.J. / Helliwell, J.R. | ||||||
![]() | ![]() Title: Direct determination of the positions of the deuterium atoms of the bound water in -concanavalin A by neutron Laue crystallography. Authors: Habash, J. / Raftery, J. / Nuttall, R. / Price, H.J. / Wilkinson, C. / Kalb, A.J. / Helliwell, J.R. #1: ![]() Title: Neutron Laue Diffraction Study of Concanavalin A:The Proton of Asp28 Authors: Habash, J. / Raftery, J. / Weisgerber, S. / Cassetta, A. / Lehmann, M.S. / Hoghoj, P. / Wilkinson, C. / Campbell, J.W. / Helliwell, J.R. #2: ![]() Title: The Structure of Concanavalin a and its Bound Solvent Determined with Small- Molecule Accuracy at 0.94A Resolution Authors: Deacon, A. / Gleichmann, T. / Kalb, A.J. / Price, H. / Raftery, J. / Bradbrook, G. / Yariv, J. / Helliwell, J.R. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 105.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 83.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 25622.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|---|
#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Sequence details | THE AMINO ACID SEQUENCE IN SWS ENTRY P02866 is the pre pro concanavalin A WHICH IS POST ...THE AMINO ACID SEQUENCE IN SWS ENTRY P02866 is the pre pro concanavalin A WHICH IS POST TRANSLATIO |
-Experimental details
-Experiment
Experiment | Method: NEUTRON DIFFRACTION / Number of used crystals: 1 |
---|
-
Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.31 % Description: NEUTRON DIFFRACTION HYDROGEN/DEUTERIUM EXCHANGE TECHNIQUE WAS EMPLOYED | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6.5 Details: CRYSTALS SELECTED FOR NEUTRON STUDY WERE TRANSFERRED TO A 1ML BUFFERMADE UP OF 99.9% D2O WITH 0.1M NANO3, 0.05M TRIS-ACETATE, 1MM MNCL2 AND 1MM CACL2; PH 6.5. | |||||||||||||||||||||
Crystal grow | *PLUS Method: batch method / Details: Greer, J., (1970) J. Mol. Biol., 48, 365. | |||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: NUCLEAR REACTOR / Site: ![]() ![]() | |||||||||
Detector | Type: FUJI Detector: CYLINDRICAL DETECTOR EIGHT IMAGE PLATE EACH 200X200 MM Date: Oct 21, 1997 | |||||||||
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 2.4→15.79 Å / Num. obs: 8605 / % possible obs: 89 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.222 / Rsym value: 0.222 / Net I/σ(I): 2.8 | |||||||||
Reflection shell | Resolution: 2.4→2.48 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 1.4 / % possible all: 82.2 | |||||||||
Reflection | *PLUS Highest resolution: 2.4 Å | |||||||||
Reflection shell | *PLUS % possible obs: 82.2 % / Num. unique obs: 773 / Rmerge(I) obs: 0.436 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.4→15.792 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→15.792 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.51 Å / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.27 / Rfactor Rfree: 0.301 / Rfactor Rwork: 0.27 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.378 / Rfactor Rwork: 0.302 |