[English] 日本語
![](img/lk-miru.gif)
- PDB-5ohf: Globin sensor domain of AfGcHK (FeIII form) in complex with cyani... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5ohf | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Globin sensor domain of AfGcHK (FeIII form) in complex with cyanide, partially reduced | ||||||||||||
![]() | Globin-coupled histidine kinase | ||||||||||||
![]() | TRANSFERASE / Heme / Sensor protein / Oxygen sensor / Globin sensor domain / globin domain / cyanide | ||||||||||||
Function / homology | ![]() peptidyl-histidine phosphorylation / histidine kinase / phosphorelay signal transduction system / phosphorelay sensor kinase activity / oxygen binding / heme binding / protein homodimerization activity / ATP binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Anaeromyxobacter sp. | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Skalova, T. / Kolenko, P. / Dohnalek, J. / Stranava, M. / Martinkova, M. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: Coordination and redox state-dependent structural changes of the heme-based oxygen sensor AfGcHK associated with intraprotein signal transduction. Authors: Stranava, M. / Man, P. / Skalova, T. / Kolenko, P. / Blaha, J. / Fojtikova, V. / Martinek, V. / Dohnalek, J. / Lengalova, A. / Rosulek, M. / Shimizu, T. / Martinkova, M. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 306.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 252.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 3.3 MB | Display | |
Data in XML | ![]() | 62.3 KB | Display | |
Data in CIF | ![]() | 86.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5oheSC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 18370.861 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: gchK, Anae109_2438 / Plasmid: pET21c(+) / Production host: ![]() ![]() |
---|
-Non-polymers , 5 types, 1038 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/CYN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CYN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-CYN / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 46 % Description: Crystal shape - red wedge block 300x80x80 um; the crystal was soaked for 15 min in a maternal drop containing additionally 10 mM sodium dithionite. |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 20.7% (w/v) PEG3350, 200 mM MgCl2, 0.01 M KCN, 7.5% (v/v) glycerol, 0.1 M MMT buffer system (DL-Malic acid, MES monohydrate, Tris, NaOH, HCl), pH 6.7 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→49.17 Å / Num. obs: 127077 / % possible obs: 100 % / Observed criterion σ(I): -3.7 / Redundancy: 7.3 % / Biso Wilson estimate: 21 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.034 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.761 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 6192 / CC1/2: 0.844 / Rpim(I) all: 0.442 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5OHE Resolution: 1.8→49.17 Å / Cor.coef. Fo:Fc: 0.958 / SU B: 2.748 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.138 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.8→49.17 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|