[English] 日本語
![](img/lk-miru.gif)
- PDB-1nto: N249Y MUTANT OF ALCOHOL DEHYDROGENASE FROM THE ARCHAEON SULFOLOBU... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1nto | ||||||
---|---|---|---|---|---|---|---|
Title | N249Y MUTANT OF ALCOHOL DEHYDROGENASE FROM THE ARCHAEON SULFOLOBUS SOLFATARICUS-MONOCLINIC CRYSTAL FORM | ||||||
![]() | NAD-dependent alcohol dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / ARCHAEON / NAD(H)-DEPENDENT / MUTANT | ||||||
Function / homology | ![]() alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Esposito, L. / Bruno, I. / Sica, F. / Raia, C.A. / Giordano, A. / Rossi, M. / Mazzarella, L. / Zagari, A. | ||||||
![]() | ![]() Title: Structural study of a single-point mutant of Sulfolobus solfataricus alcohol dehydrogenase with enhanced activity. Authors: Esposito, L. / Bruno, I. / Sica, F. / Raia, C.A. / Giordano, A. / Rossi, M. / Mazzarella, L. / Zagari, A. #1: ![]() Title: Asn249tyr substitution at the coenzyme binding domain activates Sulfolobus solfataricus alcohol dehydrogenase and increases its thermal stability Authors: Giordano, A. / Cannio, R. / La Cara, F. / Bartolucci, S. / Rossi, M. / Raia, C.A. #2: ![]() Title: Crystal structure of alcohol dehydrogenase from the hyperthermophilic archaeon Sulfolobus solfataricus at 1.85 angstrom resolution Authors: Esposito, L. / Sica, F. / Raia, C.A. / Giordano, A. / Rossi, M. / Mazzarella, L. / Zagari, A. #3: ![]() Title: Three Dimensional Structure of Horse Liver Alcoholdehydrogenase at 2.4 Angstrom Resolution Authors: Eklund, H. / Nordstrom, B. / Zeppezauer, E. / Soderlund, G. / Ohlsson, I. / Boiwe, T. / Soderberg, B.O. / Tapia, O. / Branden, C.I. / Akeson, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 401.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 329.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 483.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 533 KB | Display | |
Data in XML | ![]() | 80 KB | Display | |
Data in CIF | ![]() | 111.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1nvgC ![]() 1jvbS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a tetramer. The asymmetric unit contains six monomers. Chains ABCD form a tetramer. The second tetramer is generated from chains EH in the asymmetric unit by the operation: -x+1, y, -z+1 |
-
Components
#1: Protein | Mass: 37664.594 Da / Num. of mol.: 6 / Mutation: N249Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.68 % |
---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 7%(w/v) PEG 4000, 7%(v/v) Isopropanol, 50 mM Sodium citrate pH 5.6, 50 mM Tris pH 7.8 , 25 mM CoCl2 , VAPOR DIFFUSION, HANGING DROP, temperature 296K |
Crystal grow | *PLUS Details: Pearl, L., (1993) J. Mol. Biol., 229, 782. |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 5, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→15 Å / Num. obs: 146709 / % possible obs: 87.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 29.8 |
Reflection shell | Resolution: 1.94→2.01 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 11.7 / % possible all: 86.9 |
Reflection | *PLUS Lowest resolution: 15 Å / Num. measured all: 554277 |
Reflection shell | *PLUS % possible obs: 86.9 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 12 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1JVB Resolution: 1.94→15 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.59 Å2 / ksol: 0.4714 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.5 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.94→15 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.94→2.01 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rwork: 0.21 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|