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Yorodumi- PDB-3b2c: Crystal structure of the collagen triple helix model [{PRO-HYP(R)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b2c | ||||||
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Title | Crystal structure of the collagen triple helix model [{PRO-HYP(R)-GLY}4-{HYP(S)-Pro-GLY}2-{PRO-HYP(R)-GLY}4]3 | ||||||
Components | Collagen-like peptide | ||||||
Keywords | STRUCTURAL PROTEIN / COLLAGEN STABILITY / PUCKERING / AMINO ACID-PREFERENCES / TRIPLE HELIX | ||||||
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: 1.36 Å | ||||||
Authors | Motooka, D. / Kawahara, K. / Nakamura, S. / Doi, M. / Nishi, Y. / Nishiuchi, Y. / Nakazawa, T. / Yoshida, T. / Ohkubo, T. / Kobayashi, Y. ...Motooka, D. / Kawahara, K. / Nakamura, S. / Doi, M. / Nishi, Y. / Nishiuchi, Y. / Nakazawa, T. / Yoshida, T. / Ohkubo, T. / Kobayashi, Y. / Kang, Y.K. / Uchiyama, S. | ||||||
Citation | Journal: Biopolymers / Year: 2011 Title: The triple helical structure and stability of collagen model peptide with 4(S)-hydroxyprolyl-pro-gly units Authors: Motooka, D. / Kawahara, K. / Nakamura, S. / Doi, M. / Nishi, Y. / Nishiuchi, Y. / Kee Kang, Y. / Nakazawa, T. / Uchiyama, S. / Yoshida, T. / Ohkubo, T. / Kobayashi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b2c.cif.gz | 357.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b2c.ent.gz | 380 KB | Display | PDB format |
PDBx/mmJSON format | 3b2c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3b2c_validation.pdf.gz | 696.6 KB | Display | wwPDB validaton report |
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Full document | 3b2c_full_validation.pdf.gz | 812.8 KB | Display | |
Data in XML | 3b2c_validation.xml.gz | 45.4 KB | Display | |
Data in CIF | 3b2c_validation.cif.gz | 76.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/3b2c ftp://data.pdbj.org/pub/pdb/validation_reports/b2/3b2c | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 2690.828 Da / Num. of mol.: 9 / Source method: obtained synthetically / Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED / 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: 1.86 Å3/Da / Density % sol: 34.05 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 100mM Bicine buffer, 20% (w/v) Polyethylene glycol monomethyl ether 550, 100mM sodium chloride, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.8 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 14, 2007 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→50 Å / Num. obs: 42284 / % possible obs: 98.9 % |
Reflection shell | Resolution: 1.32→1.37 Å / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→10 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.979 / Cross valid method: THROUGHOUT / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.399 Å2
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Refinement step | Cycle: LAST / Resolution: 1.36→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.36→1.395 Å / Total num. of bins used: 20
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