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Yorodumi- PDB-1a3i: X-RAY CRYSTALLOGRAPHIC DETERMINATION OF A COLLAGEN-LIKE PEPTIDE W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a3i | ||||||
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Title | X-RAY CRYSTALLOGRAPHIC DETERMINATION OF A COLLAGEN-LIKE PEPTIDE WITH THE REPEATING SEQUENCE (PRO-PRO-GLY) | ||||||
Components | (COLLAGEN-LIKE PEPTIDE) x 2 | ||||||
Keywords | EXTRACELLULAR MATRIX / COLLAGEN | ||||||
Function / homology | ACETIC ACID Function and homology information | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | ||||||
Authors | Kramer, R.Z. / Vitagliano, L. / Bella, J. / Berisio, R. / Mazzarella, L. / Brodsky, B. / Zagari, A. / Berman, H.M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: X-ray crystallographic determination of a collagen-like peptide with the repeating sequence (Pro-Pro-Gly). Authors: Kramer, R.Z. / Vitagliano, L. / Bella, J. / Berisio, R. / Mazzarella, L. / Brodsky, B. / Zagari, A. / Berman, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a3i.cif.gz | 11.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a3i.ent.gz | 8 KB | Display | PDB format |
PDBx/mmJSON format | 1a3i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a3i_validation.pdf.gz | 413.5 KB | Display | wwPDB validaton report |
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Full document | 1a3i_full_validation.pdf.gz | 413.4 KB | Display | |
Data in XML | 1a3i_validation.xml.gz | 3.5 KB | Display | |
Data in CIF | 1a3i_validation.cif.gz | 4.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/1a3i ftp://data.pdbj.org/pub/pdb/validation_reports/a3/1a3i | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | THE 21 RESIDUE ASYMMETRIC UNIT CORRESPONDS TO ONE TRIPLE-HELICAL REPEAT AND IS SMALLER THAN THE ENTIRE 90 RESIDUE PEPTIDE DUE TO TRANSLATIONAL DISORDER ALONG THE HELICAL AXIS. THE RESULT IS A POLYMER-LIKE STRUCTURE WITH NO DEFINED ENDS. THE POLYMER STRUCTURE IS FORMED BY CONTINUATION OF THE CHAINS USING THE SYMMETRY-RELATED MOLECULES ALONG THE HELICAL AXIS. THE TVECT RECORD BELOW PRESENTS THE TRANSLATION THAT WILL GENERATE THE POLYMER. NOTE: THEREFORE, CLOSE CONTACTS BETWEEN SYMMETRY-RELATED MOLECULES ARE INTENTIONAL AND NECESSARY. INTERCHAIN HYDROGEN BONDING AT THE END OF CHAINS ALSO UTILIZES SYMMETRY-RELATED MOLECULES. THE ENTIRE 30 RESIDUE LONG PEPTIDE CAN BE GENERATED FROM THE SUBMITTED ASYMMETRIC UNIT BY APPLYING THE FOLLOWING TRANSLATIONS (USING FRACTIONAL COORDINATES): CHAIN A: TRANSLATE RESIDUES 1 - 9 BY (0 0 1), (0 0 2), AND (0 0 3) AND RESIDUES 7 - 9 BY (0 0 4). CHAIN B: TRANSLATE RESIDUES 31 - 36 BY (0 0 1), (0 0 2), AND (0 0 3). CHAIN C: TRANSLATE RESIDUES 61 - 66 BY (0 0 1), (0 0 2), AND (0 0 3) AND RESIDUES 64 - 66 BY (004). THIS WILL RESULT IN A MOLECULE WITH A TOTAL OF 90 RESIDUES, 30 IN EACH CHAIN. |
-Components
#1: Protein/peptide | Mass: 771.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source | ||||||||
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#2: Protein/peptide | Mass: 520.578 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | HYDROGEN BONDS BETWEEN PEPTIDE CHAINS FOLLOW THE RICH AND CRICK MODEL II FOR COLLAGEN. | Sequence details | FOR EACH CHAIN, RESIDUE NUMBERING CORRESPOND | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.82 % | ||||||||||||||||||||||||||||||
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Crystal grow | Details: PEPTIDE WAS CRYSTALLIZED FROM 4.0 MG/ML PEPTIDE IN 10% ACETIC ACID, 0.1% SODIUM AZIDE, AND 3.0% PEG400. | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 259 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Oct 1, 1991 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.97 Å / Num. obs: 1136 / % possible obs: 99.5 % / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.97→2.2 Å / % possible all: 98 |
Reflection | *PLUS % possible obs: 100 % |
Reflection shell | *PLUS Rmerge(I) obs: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IDEALIZED SEVEN-FOLD TRIPLE-HELIX Resolution: 1.97→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: GROUP / σ(F): 2 Details: DUE TO THE QUASI-INFINITE, AVERAGED NATURE OF THE TRIPLE HELIX, DURING REFINEMENT COVALENT BONDS ARE NECESSARY TO JOIN THE MOLECULE WITH ITS SYMMETRY MATES BOTH ABOVE IT AND BELOW IT ALONG ...Details: DUE TO THE QUASI-INFINITE, AVERAGED NATURE OF THE TRIPLE HELIX, DURING REFINEMENT COVALENT BONDS ARE NECESSARY TO JOIN THE MOLECULE WITH ITS SYMMETRY MATES BOTH ABOVE IT AND BELOW IT ALONG THE HELICAL AXIS AND TIGHT REFINEMENT CONSTRAINTS WERE MAINTAINED. THE UNIT CELL AXES WERE CHOSEN TO COINCIDE WITH A PREVIOUS STRUCTURE DETERMINATION (OKUYAMA 1981) OF THIS PEPTIDE.
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Displacement parameters | Biso mean: 15.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.97→2.04 Å / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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