[English] 日本語
Yorodumi- PDB-3abn: Crystal structure of (Pro-Pro-Gly)4-Hyp-Asp-Gly-(Pro-Pro-Gly)4 at... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3abn | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of (Pro-Pro-Gly)4-Hyp-Asp-Gly-(Pro-Pro-Gly)4 at 1.02 A | ||||||
Components | collagen-like peptide | ||||||
Keywords | STRUCTURAL PROTEIN / collagen-helix | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 Å | ||||||
Authors | Okuyama, K. / Shimura, M. / Kawaguchi, T. / Noguchi, K. / Mizuno, K. / Bachinger, H.P. | ||||||
Citation | Journal: Biopolymers / Year: 2013 Title: Crystal structure of the collagen model peptide (Pro-Pro-Gly)4 -Hyp-Asp-Gly-(Pro-Pro-Gly)4 at 1.0 angstrom resolution. Authors: Okuyama, K. / Kawaguchi, T. / Shimura, M. / Noguchi, K. / Mizuno, K. / Bachinger, H.P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3abn.cif.gz | 37.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3abn.ent.gz | 29.8 KB | Display | PDB format |
PDBx/mmJSON format | 3abn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/3abn ftp://data.pdbj.org/pub/pdb/validation_reports/ab/3abn | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein/peptide | Mass: 2313.520 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: THIS PEPTIDE WAS CHEMICALLY SYSTHESIZED. #2: Water | ChemComp-HOH / | Sequence details | THIS SEQUENCE ADOPTS COLLAGEN-HELIX | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.38 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 15% PEG 4000, 0.05M Ammonium Acetate, 0.05M Sodium Acetate Trihydrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 18, 2005 / Details: 1.1 M bent-plane mirror |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.02→22.35 Å / Num. obs: 27010 / % possible obs: 99.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.02→1.06 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 4.4 / Num. unique all: 2687 / % possible all: 99.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.02→10 Å / Num. parameters: 5737 / Num. restraintsaints: 7108 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 1 / Occupancy sum hydrogen: 410.44 / Occupancy sum non hydrogen: 625.42 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.02→10 Å
| |||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||
LS refinement shell |
|