+
Open data
-
Basic information
Entry | Database: PDB / ID: 2drt | ||||||
---|---|---|---|---|---|---|---|
Title | Structure Analysis of (POG)4-LOG-(POG)5 | ||||||
![]() | collagen like peptide | ||||||
![]() | STRUCTURAL PROTEIN / collagen / triple helix / Leu | ||||||
Function / homology | ETHANOL![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Okuyama, K. | ||||||
![]() | ![]() Title: Unique side chain conformation of a leu residue in a triple-helical structure Authors: Okuyama, K. / Narita, H. / Kawaguchi, T. / Noguchi, K. / Tanaka, Y. / Nishino, N. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 26.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 20.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 462.3 KB | Display | |
Data in XML | ![]() | 7.8 KB | Display | |
Data in CIF | ![]() | 10.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2drxC ![]() 1v4fS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein/peptide | Mass: 2706.871 Da / Num. of mol.: 3 / Source method: obtained synthetically Details: Leu-Hyp-Gly guest triplet sandwiched by host Pro-Hyp-Gly sequence; This host triplet is very popular in the collagen sequence. #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 31.93 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 12.5% PEG 400, 0.05M acetate buffer, 5.0% Ethanol, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 25, 2003 / Details: mirror |
Radiation | Monochromator: fixed-exit double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 8327 / Num. obs: 7797 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.316 / Num. unique all: 767 / % possible all: 99.6 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1V4F Resolution: 1.6→8 Å / Num. parameters: 2879 / Num. restraintsaints: 2487 / Isotropic thermal model: Isotropic / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.3 Å2 | |||||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 468.5 / Occupancy sum non hydrogen: 714 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→8 Å
| |||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||
LS refinement shell |
|