+
Open data
-
Basic information
Entry | Database: PDB / ID: 3b0s | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of (Gly-Pro-Hyp)9 | ||||||
![]() | collagen-like peptide | ||||||
![]() | STRUCTURAL PROTEIN / collagen / triple helix | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Okuyama, K. / Miyama, K. / Mizuno, K. / Bachinger, H.P. | ||||||
![]() | ![]() Title: Crystal structure of (Gly-Pro-Hyp)(9) : Implications for the collagen molecular model. Authors: Okuyama, K. / Miyama, K. / Mizuno, K. / Bachinger, H.P. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 45.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 38.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 469.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 472.4 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 19.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2drtS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein/peptide | Mass: 2423.547 Da / Num. of mol.: 6 / Source method: obtained synthetically Details: This peptide appears most frequently in native collagen. References: UniProt: Q80BK4*PLUS #2: Water | ChemComp-HOH / | Sequence details | AUTHOR STATES THE E-CHAIN CONSISTS OF TWO CHAINS WITH HALF OCCUPANCIES. THESE TWO CHAINS ARE ...AUTHOR STATES THE E-CHAIN CONSISTS OF TWO CHAINS WITH HALF OCCUPANCIE | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.34 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 22% PEG 200, 0.1M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Oct 15, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. obs: 20281 / % possible obs: 99.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 3.4 / Num. unique all: 964 / % possible all: 99.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2DRT Resolution: 1.45→8 Å / Num. parameters: 5605 / Num. restraintsaints: 4729 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 3 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 5 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1385 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|