[English] 日本語
![](img/lk-miru.gif)
- PDB-8hdn: Brucella melitensis 7-alpha-Hydroxysteroid Dehydrogenase mutant: ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8hdn | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Brucella melitensis 7-alpha-Hydroxysteroid Dehydrogenase mutant: 1-53 truncation-I258M/K262T | |||||||||
![]() | 7-alpha-hydroxysteroid dehydrogenase | |||||||||
![]() | OXIDOREDUCTASE / SDR family / hydroxysteroid dehydrogenase | |||||||||
Function / homology | 7alpha-hydroxysteroid dehydrogenase / cholate 7-alpha-dehydrogenase activity / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / 7-alpha-hydroxysteroid dehydrogenase![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Liu, Z.Y. / Zhang, R.Z. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structure of 7-alpha-hydroxysteroid dehydrogenase Authors: Liu, Z.Y. / Zhang, R.Z. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 199.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 156.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 444.9 KB | Display | |
Data in XML | ![]() | 41.6 KB | Display | |
Data in CIF | ![]() | 61.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hdeC ![]() 8hdiC ![]() 8hs4C ![]() 8hs5C ![]() 8hs6C ![]() 8hs9C ![]() 8hsaC ![]() 1fmcS ![]() 3gafS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 25872.635 Da / Num. of mol.: 4 / Fragment: 1-53 truncation Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: BMEI0406 / Production host: ![]() ![]() References: UniProt: Q8YIN7, 7alpha-hydroxysteroid dehydrogenase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.81 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1M MIB, 10% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→44.13 Å / Num. obs: 113642 / % possible obs: 99.9 % / Redundancy: 9.9 % / Biso Wilson estimate: 12.68 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.044 / Rrim(I) all: 0.139 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.7→1.763 Å / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 10.9 / Num. unique obs: 11259 / CC1/2: 0.865 / Rpim(I) all: 0.334 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3GAF, 1FMC Resolution: 1.7→33.96 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 20.44 / Stereochemistry target values: ML
| ||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→33.96 Å
| ||||||||||||||||||||
Refine LS restraints | Type: f_bond_d / Dev ideal: 0.006 / Number: 7141 | ||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.79 Å
|