[English] 日本語
![](img/lk-miru.gif)
- PDB-1d7k: CRYSTAL STRUCTURE OF HUMAN ORNITHINE DECARBOXYLASE AT 2.1 ANGSTRO... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1d7k | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF HUMAN ORNITHINE DECARBOXYLASE AT 2.1 ANGSTROMS RESOLUTION | ||||||
![]() | HUMAN ORNITHINE DECARBOXYLASE | ||||||
![]() | LYASE / ALPHA-BETA BARREL / PYRIDOXAL 5'-PHOSPHATE / SHEET-DOMAIN / DECARBOXYLATION / ORNITHINE | ||||||
Function / homology | ![]() ornithine decarboxylase / putrescine biosynthetic process from ornithine / ornithine decarboxylase activity / Metabolism of polyamines / polyamine metabolic process / Regulation of ornithine decarboxylase (ODC) / regulation of protein catabolic process / kidney development / response to virus / cell population proliferation ...ornithine decarboxylase / putrescine biosynthetic process from ornithine / ornithine decarboxylase activity / Metabolism of polyamines / polyamine metabolic process / Regulation of ornithine decarboxylase (ODC) / regulation of protein catabolic process / kidney development / response to virus / cell population proliferation / positive regulation of cell population proliferation / protein homodimerization activity / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Almrud, J.J. / Oliveira, M.A. / Kern, A.D. / Grishin, N.V. / Phillips, M.A. / Hackert, M.L. | ||||||
![]() | ![]() Title: Crystal structure of human ornithine decarboxylase at 2.1 A resolution: structural insights to antizyme binding. Authors: Almrud, J.J. / Oliveira, M.A. / Kern, A.D. / Grishin, N.V. / Phillips, M.A. / Hackert, M.L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 175.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 144 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 47161.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.86 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 7.5 Details: 20% PEG 3350, 0.2M NaCl, 5mM DTT, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, temperature 16K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Jan 15, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.908 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 55799 / Num. obs: 53656 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.09→2.16 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.363 / Num. unique all: 4929 / % possible all: 97.5 |
Reflection | *PLUS Num. measured all: 223151 |
Reflection shell | *PLUS % possible obs: 97.5 % |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.1→30.5 Å / Cross valid method: throyghout / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: This structure was refined using data from 30-2.1 angstrom resolution using the CCP4 suite program REFMAC. The REFMAC refinement was carried out using the maximum likelihood function and ...Details: This structure was refined using data from 30-2.1 angstrom resolution using the CCP4 suite program REFMAC. The REFMAC refinement was carried out using the maximum likelihood function and minimization by the conjugate direction method.
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→30.5 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
| |||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / Rfactor Rfree: 0.306 / Rfactor Rwork: 0.235 / Num. reflection obs: 6009 |