+
Open data
-
Basic information
Entry | Database: PDB / ID: 1ab1 | ||||||
---|---|---|---|---|---|---|---|
Title | SI FORM CRAMBIN | ||||||
![]() | CRAMBIN (SER22/ILE25) | ||||||
![]() | PLANT SEED PROTEIN / THIONIN | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Teeter, M.M. / Yamano, A. | ||||||
![]() | ![]() Title: Crystal structure of Ser-22/Ile-25 form crambin confirms solvent, side chain substate correlations. Authors: Yamano, A. / Heo, N.H. / Teeter, M.M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 26.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 17.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 379.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 379 KB | Display | |
Data in XML | ![]() | 2.9 KB | Display | |
Data in CIF | ![]() | 3.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein/peptide | Mass: 4728.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Species: Crambe hispanica / Strain: subsp. abyssinica / References: UniProt: P01542 |
---|---|
#2: Chemical | ChemComp-EOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.77 Å3/Da / Density % sol: 30.37 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion - hanging drop - microseeding / pH: 7 Details: HPLC PURIFIED SI-CRAMBIN PROTEIN WAS DISSOLVED AT 25 MG/ML IN 80% ETHANOL/WATER (V/V), AND EQUILIBRATED AGAINS 60% ETHANOL. AFTER 10 DAYS, THE RESERVOIR WAS LOWERED TO 50% AND MICROSEEDED BY ...Details: HPLC PURIFIED SI-CRAMBIN PROTEIN WAS DISSOLVED AT 25 MG/ML IN 80% ETHANOL/WATER (V/V), AND EQUILIBRATED AGAINS 60% ETHANOL. AFTER 10 DAYS, THE RESERVOIR WAS LOWERED TO 50% AND MICROSEEDED BY THE STREAK SEEDING METHOD (CAT WHISKER). AFTER LOWERING THE RESERVOIR TO 45%, GOOD CRYSTALS WERE FORMED., pH 7., vapor diffusion - hanging drop - microseeding | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion / Details: Teeter, M.M., (1979) J. Mol. Biol., 127, 219. | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 150 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Oct 1, 1992 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 0.89→17.67 Å / Num. obs: 23165 / % possible obs: 88.77 % / Observed criterion σ(I): 0 / Redundancy: 1 % / Rmerge(I) obs: 0.04 / Rsym value: 0.1 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 0.89→0.897 Å / Redundancy: 0.1 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.15 / % possible all: 74.96 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ALREADY SOLVED / Resolution: 0.89→10 Å / Cross valid method: DIFFERENCE DENSITY PEAKS / σ(F): 2 Details: OVERALL WEIGHT WAS 1/(SIGDEL) AND SIGDEL=8-10(SINTH/L-0.166667) THIS STRUCTURE ILLUSTRATES THE CONFIRMATION OF THE ABILITY OF X-RAY DIFFRACTION TO DETECT SUBSTATES. HERE THE SUBSTATES WERE ...Details: OVERALL WEIGHT WAS 1/(SIGDEL) AND SIGDEL=8-10(SINTH/L-0.166667) THIS STRUCTURE ILLUSTRATES THE CONFIRMATION OF THE ABILITY OF X-RAY DIFFRACTION TO DETECT SUBSTATES. HERE THE SUBSTATES WERE PHYSICALLY SEPARATED (TWO SEQUENCE FORMS OF CRAMBIN) AND SEPARATE STRUCTURES DETERMINED. FURTHER SUBSTATES ARE EXTENDED FROM PROTEIN TO SURROUNDING SOLVENT.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 5.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.08 Å / Luzzati d res low obs: 17.6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.89→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|