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Open data
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Basic information
Entry | Database: PDB / ID: 2drx | ||||||
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Title | Structure Analysis of (POG)4-(LOG)2-(POG)4 | ||||||
![]() | collagen like peptide | ||||||
![]() | STRUCTURAL PROTEIN / collagen / triple helix / Leu | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Okuyama, K. | ||||||
![]() | ![]() Title: Unique side chain conformation of a leu residue in a triple-helical structure Authors: Okuyama, K. / Narita, H. / Kawaguchi, T. / Noguchi, K. / Tanaka, Y. / Nishino, N. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 35.2 KB | Display | ![]() |
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PDB format | ![]() | 28.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.5 KB | Display | ![]() |
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Full document | ![]() | 422.7 KB | Display | |
Data in XML | ![]() | 3.9 KB | Display | |
Data in CIF | ![]() | 5.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2drtC ![]() 1v4fS C: citing same article ( 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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Unit cell |
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Components
#1: Protein/peptide | Mass: 2722.914 Da / Num. of mol.: 3 / Source method: obtained synthetically Details: Two LEU-Hyp-Gly guest triplets sandwiched by host Pro-Hyp-Gly sequence; This host triplet is very popular in the collagen sequence. #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.95 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 13.5% PEG 2000, 0.05M citrate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 25, 2004 / Details: 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: 1.4→50 Å / Num. all: 11974 / Num. obs: 10986 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.294 / Num. unique all: 1183 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1V4F Resolution: 1.4→8 Å / Num. parameters: 4655 / Num. restraintsaints: 5584 Isotropic thermal model: anisotropic for peptide, isotropic for water Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 482.5 / Occupancy sum non hydrogen: 720.5 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→8 Å
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Refine LS restraints |
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LS refinement shell |
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