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Yorodumi- PDB-1itt: Average Crystal Structure of (Pro-Pro-Gly)9 at 1.0 angstroms Reso... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1itt | ||||||
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Title | Average Crystal Structure of (Pro-Pro-Gly)9 at 1.0 angstroms Resolution | ||||||
Components | (COLLAGEN TRIPLE HELIX) x 3 | ||||||
Keywords | STRUCTURAL PROTEIN / collagen / triple helix / Pro-Pro-Gly / single crystal | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1 Å | ||||||
Authors | Hongo, C. / Nagarajan, V. / Noguchi, K. / Kamitori, S. / Okuyama, K. / Tanaka, Y. / Nishino, N. | ||||||
Citation | Journal: Plym.J. / Year: 2001 Title: Average Crystal Structure of (Pro-Pro-Gly)9 at 1.0 angstroms Resolution Authors: Hongo, C. / Nagarajan, V. / Noguchi, K. / Kamitori, S. / 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 | 1itt.cif.gz | 10 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1itt.ent.gz | 7 KB | Display | PDB format |
PDBx/mmJSON format | 1itt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1itt_validation.pdf.gz | 341.2 KB | Display | wwPDB validaton report |
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Full document | 1itt_full_validation.pdf.gz | 341.2 KB | Display | |
Data in XML | 1itt_validation.xml.gz | 1.6 KB | Display | |
Data in CIF | 1itt_validation.cif.gz | 2.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/1itt ftp://data.pdbj.org/pub/pdb/validation_reports/it/1itt | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | THE ENTIRE 27 RESIDUE LONG PEPTIDE CAN BE GENERATED FROM THE SUBMITTED ASYMMETRIC UNIT BY APPLYING THE FOLLOWING TRANSLATIONS (USING FRACTIONAL COORDINATES): CHAIN A: TRANSLATE RESIDUES 2 - 7 BY (0 0 1), AND RESIDUES 1-7 BY (002), (003), (004) AND RESIDUE 1 BY (005). CHAIN B: TRANSLATE RESIDUES 33-37 BY (0 0 1), AND RESIDUES 31-37 BY (002), (003), (004) AND RESIDUE 31-32 BY (005). CHAIN C: TRANSLATE RESIDUES 64-67 BY (0 0 1), AND RESIDUES 61-67 BY (002), (003), (004). THIS WILL RESULT IN A MOLECULE WITH A TOTAL OF 81 RESIDUES, 27 IN EACH CHAIN. |
-Components
#1: Protein/peptide | Mass: 577.630 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in collagens. |
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#2: Protein/peptide | Mass: 617.693 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in collagens. |
#3: Protein/peptide | Mass: 617.693 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in collagens. |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.13 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop Details: PEG400, acetic acid, sodium azide, VAPOR DIFFUSION, HANGING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU AFC-5R / Detector: DIFFRACTOMETER / Date: May 18, 1999 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1→8 Å / Num. all: 6129 / Num. obs: 2922 / Observed criterion σ(F): 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: The structural model for collagen proposed by Okuyama (1981) Resolution: 1→8 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1→8 Å
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Refine LS restraints |
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