[English] 日本語
![](img/lk-miru.gif)
- PDB-3cot: Crystal structure of human liver delta(4)-3-ketosteroid 5beta-red... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3cot | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human liver delta(4)-3-ketosteroid 5beta-reductase (akr1d1) in complex with progesterone and nadp. Resolution: 2.03 A. | ||||||
![]() | 3-oxo-5-beta-steroid 4-dehydrogenase | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() Delta4-3-oxosteroid 5beta-reductase / steroid dehydrogenase activity / C21-steroid hormone metabolic process / bile acid catabolic process / Delta4-3-oxosteroid 5beta-reductase activity / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Di Costanzo, L. / Drury, J. / Penning, T.M. / Christianson, D.W. | ||||||
![]() | ![]() Title: Crystal Structure of Human Liver {Delta}4-3-Ketosteroid 5{beta}-Reductase (AKR1D1) and Implications for Substrate Binding and Catalysis. Authors: Di Costanzo, L. / Drury, J.E. / Penning, T.M. / Christianson, D.W. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 158.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 122.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3burSC ![]() 3buvC ![]() 3bv7C ![]() 3cmfC C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 39599.258 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P51857, Delta4-3-oxosteroid 5beta-reductase #2: Chemical | ![]() #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.38 % |
---|---|
Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: isopropanol 10%,peg 4000, tris-HCl 100 mM pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 28, 2008 Details: Rosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.03→50 Å / Num. all: 45518 / Num. obs: 44101 / % possible obs: 97.6 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.03→2.15 Å / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2 / Num. unique all: 4301 / % possible all: 96.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: 3bur Resolution: 2.03→25.04 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 71162.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 74.5085 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.9 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.03→25.04 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.03→2.16 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|