+
Open data
-
Basic information
Entry | Database: PDB / ID: 8bfd | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Racemic structure of PK-7 (310HD-U2U5) | |||||||||
![]() |
| |||||||||
![]() | ![]() ![]() | |||||||||
Function / homology | DI(HYDROXYETHYL)ETHER / polypeptide(D) / polypeptide(D) (> 10)![]() | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Kumar, P. / Paterson, N.G. / Woolfson, D.N. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: De novo design of discrete, stable 3 10 -helix peptide assemblies. Authors: Kumar, P. / Paterson, N.G. / Clayden, J. / Woolfson, D.N. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 33.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 26.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7qdiC ![]() 7qdjC ![]() 7qdkC ![]() 8bfeC C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein/peptide | Mass: 3121.721 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||||
---|---|---|---|---|---|---|---|
#2: Polypeptide(D) | Mass: 3116.685 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||||
#3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-PEG / | ![]() #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.71 Å3/Da / Density % sol: 28.26 % |
---|---|
Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.12M Ethylene glycols, 0.1M (1.0M, pH 8.5 Tris (base); BICINE), 30% v/v (40% v/v PEG 500* MME; 20 % w/v PEG 20000) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 11, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→23.1 Å / Num. obs: 2744 / % possible obs: 98.75 % / Redundancy: 3.7 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.056 / Net I/σ(I): 23.29 |
Reflection shell | Resolution: 2→2.072 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.1358 / Mean I/σ(I) obs: 10.42 / Num. unique obs: 270 / CC1/2: 0.993 / CC star: 0.998 / % possible all: 99.26 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 40.15 Å2 / Biso mean: 13.597 Å2 / Biso min: 4.85 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→23.1 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|