[English] 日本語
Yorodumi- PDB-6dy8: Mn(II)-bound structure of the engineered cyt cb562 variant, CH2EY -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dy8 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Mn(II)-bound structure of the engineered cyt cb562 variant, CH2EY | |||||||||
Components | Soluble cytochrome b562 | |||||||||
Keywords | METAL BINDING PROTEIN / Designed protein / 4-helix bundle / electron transport | |||||||||
Function / homology | Function and homology information electron transfer activity / periplasmic space / iron ion binding / heme binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Tezcan, F.A. / Rittle, J. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Nat.Chem. / Year: 2019 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: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6dy8.cif.gz | 106.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6dy8.ent.gz | 81.2 KB | Display | PDB format |
PDBx/mmJSON format | 6dy8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/6dy8 ftp://data.pdbj.org/pub/pdb/validation_reports/dy/6dy8 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6dy4C 6dy6C 6dybC 6dycC 6dydC 6dyeC 6dyfC 6dygC 6dyhC 6dyiC 6dyjC 6dykC 6dylC 2bc5S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 11913.368 Da / Num. of mol.: 4 / Mutation: K59W, I67H, G70Y, Q71H, T96C, T97E, R98C, Y101C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cybC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ABE7 #2: Chemical | ChemComp-HEC / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 44.97 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Drop consists of 1 uL of 25% PEG 1500, 200 mM Calcium Chloride, and 0.1 M Tris (pH 8.5) mixed with 1 uL of 3.5 mM protein and 3.5 mM Manganese(II)Chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→37.59 Å / Num. obs: 33090 / % possible obs: 98 % / Redundancy: 2.7 % / CC1/2: 0.978 / Rmerge(I) obs: 0.134 / Net I/σ(I): 3.2 |
Reflection shell | Resolution: 1.9→1.9514 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 1 / Num. unique obs: 3296 / CC1/2: 0.832 / % possible all: 98.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2bc5 Resolution: 1.9→37.59 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.76
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→37.59 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|