+
Open data
-
Basic information
Entry | Database: PDB / ID: 7o38 | ||||||
---|---|---|---|---|---|---|---|
Title | cytochrome C kustc0562 from Kuenenia stuttgartiensis | ||||||
![]() | Cytochrome c-552 Ks_3357 | ||||||
![]() | ELECTRON TRANSPORT / anaerobic ammonium oxidation / cytochrome c / redox protein | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Bock, J. / Akram, M. / Barends, T. | ||||||
![]() | ![]() Title: Specificity of Small c -Type Cytochromes in Anaerobic Ammonium Oxidation. Authors: Akram, M. / Bock, J. / Dietl, A. / Barends, T.R.M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 37.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 19.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 803.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 803.4 KB | Display | |
Data in XML | ![]() | 5.5 KB | Display | |
Data in CIF | ![]() | 6.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mxySC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 10236.707 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
---|---|
#2: Chemical | ChemComp-HEC / |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-IMD / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.13 Å3/Da / Density % sol: 70.19 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2 M NaCl, 30% w/v PEG 8000, 0.1 M imidazole pH 8.0, 0.277 mM cyclohexylethanoyl-N-hydroxyethylglucamide |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 1, 2018 / Details: KB MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→44.02 Å / Num. obs: 3395 / % possible obs: 95.8 % / Redundancy: 2.4 % / Biso Wilson estimate: 33.72 Å2 / CC1/2: 0.973 / Rmerge(I) obs: 0.037 / Rrim(I) all: 0.041 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 3→3.1 Å / Rmerge(I) obs: 0.166 / Num. unique obs: 307 / CC1/2: 0.745 / Rsym value: 0.174 |
-
Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5MXY Resolution: 3→40 Å / SU ML: 0.3025 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.8003 Stereochemistry target values: GeoStd + Monomer Library + 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: 22.21 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→40 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.1 Å
|