[English] 日本語
![](img/lk-miru.gif)
- PDB-1x1k: Host-guest peptide (Pro-Pro-Gly)4-(Pro-alloHyp-Gly)-(Pro-Pro-Gly)4 -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1x1k | ||||||
---|---|---|---|---|---|---|---|
Title | Host-guest peptide (Pro-Pro-Gly)4-(Pro-alloHyp-Gly)-(Pro-Pro-Gly)4 | ||||||
![]() | (Host-guest peptide (Pro-Pro-Gly)4-(Pro-alloHyp-Gly)-(Pro-Pro-Gly)4) x 2 | ||||||
![]() | STRUCTURAL PROTEIN / allo-Hyp / non-natural amino acid / collagen model peptide / puckering / triple-helix stability | ||||||
Function / homology | Saimiri transformation-associated protein / extracellular matrix structural constituent conferring tensile strength / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / extracellular matrix organization / extracellular space / membrane / Saimiri transformation-associated protein![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jiravanichanun, N. / Hongo, C. / Wu, G. / Noguchi, K. / Okuyama, K. / Nishino, N. / Silva, T. | ||||||
![]() | ![]() Title: Unexpected puckering of hydroxyproline in the guest triplets, hyp-pro-gly and pro-allohyp-gly sandwiched between pro-pro-gly sequence Authors: Jiravanichanun, N. / Hongo, C. / Wu, G. / Noguchi, K. / Okuyama, K. / Nishino, N. / Silva, T. #1: ![]() Title: High Resolution Structure of Collagen Model Peptide Sequence (Pro-Pro-Gly)4-(Pro-alloHyp-Gly)-(Pro-Pro-Gly)4 Authors: Jiravanichanun, N. / Noguchi, K. / Okuyama, K. / Nishino, N. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 68.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 55.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 381.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 382 KB | Display | |
Data in XML | ![]() | 4.3 KB | Display | |
Data in CIF | ![]() | 8.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ittS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein/peptide | Mass: 2295.547 Da / Num. of mol.: 5 / Source method: obtained synthetically / Details: collagen model peptide was chemically systhesized / References: UniProt: Q80BK4*PLUS #2: Protein/peptide | | Mass: 2562.828 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: collagen model peptide was chemically systhesized / References: UniProt: Q80BK4*PLUS #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.74 Å3/Da / Density % sol: 29.3 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG200, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 21, 2004 | |||||||||
Radiation | Monochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 1.1→30 Å / Num. all: 43582 / Num. obs: 43437 / % possible obs: 99.67 % / Observed criterion σ(F): 1 | |||||||||
Reflection shell | Resolution: 1.1→1.14 Å / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4376 / % possible all: 99.9 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 1ITT Resolution: 1.1→8 Å / Num. parameters: 11488 / Num. restraintsaints: 15246 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 1 / Occupancy sum hydrogen: 855 / Occupancy sum non hydrogen: 1258 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→8 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|