[English] 日本語
![](img/lk-miru.gif)
- PDB-1roz: Deoxyhypusine synthase holoenzyme in its low ionic strength, high... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1roz | ||||||
---|---|---|---|---|---|---|---|
Title | Deoxyhypusine synthase holoenzyme in its low ionic strength, high pH crystal form | ||||||
![]() | Deoxyhypusine synthase | ||||||
![]() | TRANSFERASE / Rossmann Fold / NAD cofactor / deoxyhypusine / hypusine / spermidine | ||||||
Function / homology | ![]() deoxyhypusine synthase / Hypusine synthesis from eIF5A-lysine / peptidyl-lysine modification to peptidyl-hypusine / deoxyhypusine synthase activity / spermidine metabolic process / spermidine catabolic process / positive regulation of T cell proliferation / glucose homeostasis / translation / positive regulation of cell population proliferation ...deoxyhypusine synthase / Hypusine synthesis from eIF5A-lysine / peptidyl-lysine modification to peptidyl-hypusine / deoxyhypusine synthase activity / spermidine metabolic process / spermidine catabolic process / positive regulation of T cell proliferation / glucose homeostasis / translation / positive regulation of cell population proliferation / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Umland, T.C. / Wolff, E.C. / Park, M.-H. / Davies, D.R. | ||||||
![]() | ![]() Title: A New Crystal Structure of Deoxyhypusine Synthase Reveals the Configuration of the Active Enzyme and of an Enzyme-NAD-Inhibitor Ternary Complex Authors: Umland, T.C. / Wolff, E.C. / Park, M.-H. / Davies, D.R. #1: ![]() Title: Crystal structure of the NAD complex of human deoxyhypusine synthase: an enzyme with a ball-and-chain mechanism for blocking the active site Authors: Liao, D.I. / Wolff, E.C. / Park, M.-H. / Davies, D.R. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 151 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 118 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 30.6 KB | Display | |
Data in CIF | ![]() | 43.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1rlzC ![]() 1rqdC ![]() 1dhsS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a tetramer, and may be generated from the dimer contained within the asymmetric unit by the crystallographic two fold axis: x-y, -y, -z+1/3 |
-
Components
#1: Protein | Mass: 41012.434 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.11 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Tris-HCl, KCl, NAD, 2-methyl-2,4-pentanediol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 17, 1999 / Details: monochromator |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→35 Å / Num. all: 50963 / Num. obs: 50963 / % possible obs: 99.9 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 3.85 % / Biso Wilson estimate: 19.6 Å2 / Rsym value: 0.08 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.21→2.29 Å / Redundancy: 3.4 % / Num. unique all: 4949 / Rsym value: 0.303 / % possible all: 99.3 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB Entry 1DHS Resolution: 2.21→35 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: NCS restraints employed
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 29 Å2 | |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.21→35 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.21→2.29 Å / Rfactor Rfree error: 0.022
|