+
Open data
-
Basic information
Entry | Database: PDB / ID: 6dyc | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Co(II)-bound structure of the engineered cyt cb562 variant, CH3 | |||||||||
![]() | Soluble cytochrome b562 | |||||||||
![]() | METAL BINDING PROTEIN / ![]() ![]() | |||||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Tezcan, F.A. / Rittle, J. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: An efficient, step-economical strategy for the design of functional metalloproteins. Authors: Rittle, J. / Field, M.J. / Green, M.T. / Tezcan, F.A. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 102.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 78.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6dy4C ![]() 6dy6C ![]() 6dy8C ![]() 6dybC ![]() 6dydC ![]() 6dyeC ![]() 6dyfC ![]() 6dygC ![]() 6dyhC ![]() 6dyiC ![]() 6dyjC ![]() 6dykC ![]() 6dylC ![]() 2bc5S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 11816.279 Da / Num. of mol.: 2 / Mutation: K59W, I67H, Q71H, T96C, T97H, R98C, Y101C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CO / | #3: Chemical | ![]() #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.48 % |
---|---|
Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Drop consists of 2 uL of 25% PEG 3350, 200 mM Magnesium Chloride and 0.1 M Bis-Tris (pH 5.5) mixed with 2 uL of 3 mM protein and 3 mM Cobalt(II) Chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.33→38.515 Å / Num. obs: 46653 / % possible obs: 94.9 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.33→1.3633 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3702 / CC1/2: 0.772 / % possible all: 93 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: 2bc5 Resolution: 1.33→38.515 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.43
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.33→38.515 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|