+Open data
-Basic information
Entry | Database: PDB / ID: 2drx | ||||||
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Title | Structure Analysis of (POG)4-(LOG)2-(POG)4 | ||||||
Components | collagen like peptide | ||||||
Keywords | STRUCTURAL PROTEIN / collagen / triple helix / Leu | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Okuyama, K. | ||||||
Citation | Journal: Biopolymers / Year: 2007 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2drx.cif.gz | 35.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2drx.ent.gz | 28.2 KB | Display | PDB format |
PDBx/mmJSON format | 2drx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2drx_validation.pdf.gz | 422.5 KB | Display | wwPDB validaton report |
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Full document | 2drx_full_validation.pdf.gz | 422.7 KB | Display | |
Data in XML | 2drx_validation.xml.gz | 3.9 KB | Display | |
Data in CIF | 2drx_validation.cif.gz | 5.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/2drx ftp://data.pdbj.org/pub/pdb/validation_reports/dr/2drx | HTTPS FTP |
-Related structure data
Related structure data | 2drtC 1v4fS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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