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- PDB-3ai6: Triple-helical structure of (D-Pro-D-Pro-Gly)9 at 1.1 A resolution -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ai6 | ||||||
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Title | Triple-helical structure of (D-Pro-D-Pro-Gly)9 at 1.1 A resolution | ||||||
![]() | collagen-like peptide | ||||||
![]() | STRUCTURAL PROTEIN / collagen helix / D-enantiomer | ||||||
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. / Kawaguchi, T. / Nishino, N. | ||||||
![]() | ![]() Title: Triple-helical structure of (D-Pro-D-Pro-Gly)9 Authors: Okuyama, K. / Miyama, K. / Kawaguchi, T. / Nishino, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.7 KB | Display | ![]() |
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PDB format | ![]() | 66.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.4 KB | Display | ![]() |
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Full document | ![]() | 444.9 KB | Display | |
Data in XML | ![]() | 9.6 KB | Display | |
Data in CIF | ![]() | 14.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2cuoS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein/peptide | Mass: 2279.547 Da / Num. of mol.: 6 / Source method: obtained synthetically Details: This peptide adopts a collagen-helix with opposite chirality. References: UniProt: Q80BK4*PLUS #2: Water | ChemComp-HOH / | Sequence details | THE AUTHOR STATES, FOR THE SIX PEPTIDES, THE ACTUAL PEPTIDE CHAIN CONSISTS OF 27 AMINO ACID ...THE AUTHOR STATES, FOR THE SIX PEPTIDES, THE ACTUAL PEPTIDE CHAIN CONSISTS OF 27 AMINO ACID RESIDUES. THE B/F CHAIN CONSISTS OF TWO CHAINS WITH HALF OCCUPANCIE | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.62 Å3/Da / Density % sol: 38.57 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 11% PEG 200, 0.1M acetate buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Dec 8, 2009 Details: A double-crystal monochromator and a horizontal focusing Mirror |
Radiation | Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection twin | Operator: h,-k,-l / Fraction: 0.484 |
Reflection | Resolution: 1.04→50 Å / Num. obs: 50349 / % possible obs: 96.1 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 10.19 |
Reflection shell | Resolution: 1.04→1.06 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.72 / Num. unique all: 2337 / % possible all: 89.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2CUO Resolution: 1.1→10 Å / Num. parameters: 11227 / Num. restraintsaints: 14206 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber Details: The structure was refined under the twinning operator (h, -k, -l) AND TWINNING FRACTION 0.484 using the twinned data.
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1190.5 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→10 Å
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Refine LS restraints |
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LS refinement shell |
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