[English] 日本語
![](img/lk-miru.gif)
- PDB-8eh2: Short-chain dehydrogenase/reductase (SDR) from Acinetobacter baumannii -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8eh2 | ||||||
---|---|---|---|---|---|---|---|
Title | Short-chain dehydrogenase/reductase (SDR) from Acinetobacter baumannii | ||||||
![]() | SDR family oxidoreductase | ||||||
![]() | OXIDOREDUCTASE / Short-chain / SDR | ||||||
Function / homology | 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / SDR family oxidoreductase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shaw, K. | ||||||
Funding support | 1items
| ||||||
![]() | ![]() Title: Short-chain dehydrogenase/reductase (SDR) from Acinetobacter baumannii Authors: Forwood, J.K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 231.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 153.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 426.8 KB | Display | |
Data in XML | ![]() | 20.7 KB | Display | |
Data in CIF | ![]() | 29.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2d1yS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||
Components on special symmetry positions |
| |||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 1 - 259 / Label seq-ID: 1 - 259
|
-
Components
#1: Protein | Mass: 27827.480 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: 2.27 Å3/Da / Density % sol: 45.81 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2M lithium chloride, 0.1M Tris pH 8.0, 20% (v/v) polyethylene glycol 8,000 |
-Data collection
Diffraction | Mean temperature: 298 K / Ambient temp details: 80 / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→29.4 Å / Num. obs: 20194 / % possible obs: 99.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 24.95 Å2 / CC1/2: 0.986 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.4→2.49 Å / Num. unique obs: 2085 / CC1/2: 0.819 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2D1Y Resolution: 2.4→29.4 Å / SU ML: 0.2284 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5445 / Stereochemistry target values: CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→29.4 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|