+Open data
-Basic information
Entry | Database: PDB / ID: 2cuo | ||||||
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Title | Collagen model peptide (PRO-PRO-GLY)9 | ||||||
Components | COLLAGEN MODEL PEPTIDE (PRO-PRO-GLY)9 | ||||||
Keywords | STRUCTURAL PROTEIN / COLLAGEN MODEL PEPTIDE / TRIPLE-HELIX / PUCKERING | ||||||
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 Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å | ||||||
Authors | Hongo, C. / Noguchi, K. / Okuyama, K. / Tanaka, Y. / Nishino, N. | ||||||
Citation | Journal: J.Biochem.(Tokyo) / Year: 2005 Title: Repetitive interactions observed in the crystal structure of a collagen-model peptide, [(Pro-Pro-Gly)9]3 Authors: Hongo, C. / Noguchi, K. / Okuyama, 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 | 2cuo.cif.gz | 61 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cuo.ent.gz | 48.3 KB | Display | PDB format |
PDBx/mmJSON format | 2cuo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cuo_validation.pdf.gz | 371.4 KB | Display | wwPDB validaton report |
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Full document | 2cuo_full_validation.pdf.gz | 371.8 KB | Display | |
Data in XML | 2cuo_validation.xml.gz | 3.6 KB | Display | |
Data in CIF | 2cuo_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cu/2cuo ftp://data.pdbj.org/pub/pdb/validation_reports/cu/2cuo | HTTPS FTP |
-Related structure data
Related structure data | 1ittS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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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: COLLAGEN MODEL PEPTIDE WAS CHEMICALLY SYSTHESIZED / References: UniProt: Q80BK4*PLUS #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: 1.71 Å3/Da / Density % sol: 27.9 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: PEG400, ACETIC ACID, SODIUM AZIDE, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 20, 2001 / Details: 1-M-LONG BENT-CYLINDER MIRROR |
Radiation | Monochromator: FIXED-EXIT DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→25.21 Å / Num. obs: 24336 / % possible obs: 97.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 1.33→1.38 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 1.8 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ITT Resolution: 1.33→8 Å / Num. parameters: 9953 / Num. restraintsaints: 12321 / σ(F): 1 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT REDUCED FREE R
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 918 / Occupancy sum non hydrogen: 1290 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.33→8 Å
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Refine LS restraints |
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