+Open data
-Basic information
Entry | Database: PDB / ID: 5k68 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Designed Artificial Cupredoxins | |||||||||
Components | Streptavidin | |||||||||
Keywords | BIOTIN BINDING PROTEIN / beta-barrel / tetramer / cupredoxin / artificial metalloprotein / copper protein | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Streptomyces avidinii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | |||||||||
Authors | Mann, S.I. / Heinisch, T. / Weitz, A.C. / Hendrich, M.R. / Ward, T.R. / Borovik, A.S. | |||||||||
Funding support | United States, 1items
| |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2016 Title: Modular Artificial Cupredoxins. Authors: Mann, S.I. / Heinisch, T. / Weitz, A.C. / Hendrich, M.P. / Ward, T.R. / Borovik, A.S. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5k68.cif.gz | 68 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5k68.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 5k68.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5k68_validation.pdf.gz | 679.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5k68_full_validation.pdf.gz | 684.4 KB | Display | |
Data in XML | 5k68_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 5k68_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/5k68 ftp://data.pdbj.org/pub/pdb/validation_reports/k6/5k68 | HTTPS FTP |
-Related structure data
Related structure data | 5k67C 5l3yC 5wbcC 2qcbS 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: 16586.082 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629 |
---|---|
#2: Chemical | ChemComp-SI9 / [ |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.58 % |
---|---|
Crystal grow | Temperature: 274 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 2.0 M ammonium sulfate, 0.1 M sodium acetate, pH 4 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→45.9 Å / Num. obs: 31080 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 1 / Rmerge(I) obs: 0.069 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.446 / % possible all: 98.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2qcb Resolution: 1.4→45.9 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.988 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.048 / 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: 20.519 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.4→45.9 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|