[English] 日本語
Yorodumi- PDB-6x8x: Cu-bound structure of an engineered metal-dependent protein trime... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6x8x | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cu-bound structure of an engineered metal-dependent protein trimer, TriCyt1 | |||||||||
Components | Soluble cytochrome b562 | |||||||||
Keywords | METAL BINDING PROTEIN / four-helix bundle / metalloprotein trimer | |||||||||
Function / homology | Function and homology information electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.505 Å | |||||||||
Authors | Tezcan, F.A. / Kakkis, A. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2020 Title: Metal-Templated Design of Chemically Switchable Protein Assemblies with High-Affinity Coordination Sites. Authors: Kakkis, A. / Gagnon, D. / Esselborn, J. / Britt, R.D. / Tezcan, F.A. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6x8x.cif.gz | 39.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6x8x.ent.gz | 24.6 KB | Display | PDB format |
PDBx/mmJSON format | 6x8x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6x8x_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6x8x_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6x8x_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 6x8x_validation.cif.gz | 8.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/6x8x ftp://data.pdbj.org/pub/pdb/validation_reports/x8/6x8x | HTTPS FTP |
-Related structure data
Related structure data | 6wyuC 6wz0C 6wz1C 6wz2C 6wz3C 6wz7C 6wzaC 6wzcC 6x7eC 2bc5S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 11854.326 Da / Num. of mol.: 1 / Mutation: K59H, D66N, G70W, D73H, K77H, R98C, Y101C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cybC / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABE7 | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-HEC / | ||||
#3: Chemical | ChemComp-CU / | ||||
#4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.88 Å3/Da / Density % sol: 68.32 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 25% PEG2000, 200 mM CaCl2, 100 mM TRIS (pH 8.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97741 Å / Relative weight: 1 |
Reflection | Resolution: 2.505→39.8398 Å / Num. obs: 12469 / % possible obs: 99.5 % / Redundancy: 19.5 % / CC1/2: 1 / Rmerge(I) obs: 0.04198 / Rpim(I) all: 0.009792 / Rrim(I) all: 0.04313 / Net I/σ(I): 53.1 |
Reflection shell | Resolution: 2.505→2.595 Å / Redundancy: 20 % / Rmerge(I) obs: 0.2077 / Num. unique obs: 2010 / CC1/2: 0.997 / Rpim(I) all: 0.04725 / Rrim(I) all: 0.2131 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2bc5 Resolution: 2.505→39.8398 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 38.83 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.505→39.8398 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|