+
Open data
-
Basic information
Entry | Database: PDB / ID: 3adm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of (Pro-Pro-Gly)4-Hyp-Ser-Gly-(Pro-Pro-Gly)4 | ||||||
![]() | collagen-like peptide | ||||||
![]() | STRUCTURAL PROTEIN / collagen / triple helix / model peptide | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Okuyama, K. / Miyama, K. / Masakiyo, K. / Mizuno, K. / Bachinger, H.P. | ||||||
![]() | ![]() Title: Stabilization of triple-helical structures of collagen peptides containing a Hyp-Thr-Gly, Hyp-Val-Gly, or Hyp-Ser-Gly sequence. Authors: Okuyama, K. / Miyama, K. / Morimoto, T. / Masakiyo, K. / Mizuno, K. / Bachinger, H.P. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 70.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 56.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 450.6 KB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 16.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3a0mC ![]() 3a1hC ![]() 2cuoS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein/peptide | Mass: 2285.510 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: THIS PEPTIDE WAS CHEMICALLY SYSTHESIZED. #2: Water | ChemComp-HOH / | Sequence details | THIS SEQUENCE ADOPTS COLLAGEN-HELIX. THE AUTHOR STATES THAT CHAIN E HAS A DISORDERED STRUCTURE IN ...THIS SEQUENCE ADOPTS COLLAGEN-HELIX. THE AUTHOR STATES THAT CHAIN E HAS A DISORDERED | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.73 Å3/Da / Density % sol: 38.8 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 11.3% PEG 2000, 0.05M acetate buffer, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Jun 29, 2009 Details: double-crystal monochromator & horizontal focusing mirror |
Radiation | Monochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→50 Å / Num. obs: 34897 / % possible obs: 96.1 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.046 |
Reflection shell | Resolution: 1.18→1.2 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.313 / Num. unique all: 1292 / % possible all: 70.6 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2CUO Resolution: 1.18→50 Å / Num. parameters: 11326 / Num. restraintsaints: 15805 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 16 / Occupancy sum hydrogen: 846.9 / Occupancy sum non hydrogen: 1229.35 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.18→50 Å
| |||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||
LS refinement shell |
|