+
Open data
-
Basic information
Entry | Database: PDB / ID: 1qu4 | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI ORNITHINE DECARBOXYLASE | ||||||
![]() | ORNITHINE DECARBOXYLASE | ||||||
![]() | LYASE / POLYAMINE METABOLISM / PYRIDOXAL 5'-PHOSPHATE / ALPHA-BETA BARREL | ||||||
Function / homology | ![]() ornithine decarboxylase / putrescine biosynthetic process from ornithine / ornithine decarboxylase activity / polyamine biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Grishin, N.V. / Osterman, A.L. / Brooks, H.B. / Phillips, M.A. / Goldsmith, E.J. | ||||||
![]() | ![]() Title: X-ray structure of ornithine decarboxylase from Trypanosoma brucei: the native structure and the structure in complex with alpha-difluoromethylornithine. Authors: Grishin, N.V. / Osterman, A.L. / Brooks, H.B. / Phillips, M.A. / Goldsmith, E.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 277.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 231.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 486.5 KB | Display | |
Data in XML | ![]() | 36.1 KB | Display | |
Data in CIF | ![]() | 51.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a dimer constructued from chains A and B, or chains C and D |
-
Components
#1: Protein | Mass: 47062.461 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-PLP / |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.17 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 16% PEG 3350, 0.2 M SOLIUM ACETATE, 100MM HEPES 20MG/ML PROTEIN DILUTED TWICE, pH 7.5, VAPOR DIFFUSION, SITTING DROP | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging dropDetails: Grishin, N.V., (1996) Proteins Struct. Funct. Genet., 24, 272. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 90 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. all: 36421 / Num. obs: 36421 / % possible obs: 98.6 % / Observed criterion σ(F): -1000 / Observed criterion σ(I): -1000 / Redundancy: 3.3 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3 % / Rmerge(I) obs: 0.14 / % possible all: 75.3 |
Reflection | *PLUS Num. measured all: 120960 |
Reflection shell | *PLUS % possible obs: 75.3 % / Mean I/σ(I) obs: 5 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.9→20 Å / σ(F): 0 / σ(I): 0
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→20 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 8 Å / σ(F): 0 / Rfactor obs: 0.23 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |