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Yorodumi- PDB-1v6q: Crystal Structures of Collagen Model Peptides with Pro-Hyp-Gly Se... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v6q | ||||||
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Title | Crystal Structures of Collagen Model Peptides with Pro-Hyp-Gly Sequence at 1.3 A | ||||||
Components | (Collagen like peptide) x 3 | ||||||
Keywords | STRUCTURAL PROTEIN / Collagen / Triple-helix / Model peptide | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Okuyama, K. / Hongo, C. / Fukushima, R. / Wu, G. / Narita, H. / Noguchi, K. / Tanaka, Y. / Nishino, N. | ||||||
Citation | Journal: Biopolymers / Year: 2004 Title: Crystal structures of collagen model peptides with Pro-Hyp-Gly repeating sequence at 1.26 A resolution: implications for proline ring puckering Authors: Okuyama, K. / Hongo, C. / Fukushima, R. / Wu, G. / Narita, H. / 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 | 1v6q.cif.gz | 15.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v6q.ent.gz | 11.1 KB | Display | PDB format |
PDBx/mmJSON format | 1v6q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1v6q_validation.pdf.gz | 362.5 KB | Display | wwPDB validaton report |
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Full document | 1v6q_full_validation.pdf.gz | 362.5 KB | Display | |
Data in XML | 1v6q_validation.xml.gz | 1.8 KB | Display | |
Data in CIF | 1v6q_validation.cif.gz | 2.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v6/1v6q ftp://data.pdbj.org/pub/pdb/validation_reports/v6/1v6q | 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 ENTIRE 33 RESIDUE LONG PEPTIDE CAN BE GENERATED FROM THE SUBMITTED ASYMMETRIC UNIT BY APPLYING THE FOLLOWING TRANSLATIONS (USING FRACTIONAL COORDINATES): CHAIN A: TRANSLATE RESIDUES 104-109 BY (001), AND RESIDUES 103-109 BY (002), (003), (004)(005). CHAIN B: TRANSLATE RESIDUES 204 - 208 BY (001), AND RESIDUES 202-208 BY (002), (003), (004) AND RESIDUE 202-206 BY (005). CHAIN C: TRANSLATE RESIDUES 301 - 307 BY (001), (002), (003) (004), AND RESIDUES 301-306 BY (005). THIS WILL RESULT IN A MOLECULE WITH A TOTAL OF 99 RESIDUES, 33 IN EACH CHAIN. |
-Components
#1: Protein/peptide | Mass: 609.630 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: (Pro-Hyp-Gly) triplet is very popular in collagen sequence |
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#2: Protein/peptide | Mass: 665.693 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: (Pro-Hyp-Gly) triplet is very popular in collagen sequence |
#3: Protein/peptide | Mass: 649.693 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: (Pro-Hyp-Gly) triplet is very popular in collagen sequence |
#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: 1.87 Å3/Da / Density % sol: 34.28 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: PEG 200, Acetic acid, Sodium azide, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 25, 2002 / 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: 1.25→19.15 Å / Num. obs: 3768 / % possible obs: 94.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.25→1.3 Å / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 2.4 / Num. unique all: 268 / % possible all: 67.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: (Pro-Hyp-Gly)10 structure reported in V.Nagarajan, S.Kamitori and K.Okuyama, J.Biochem., 125, 310 (1999). Resolution: 1.25→10 Å / Num. parameters: 1368 / Num. restraintsaints: 1698 / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: Engh & Huber Details: The polymer structure can be generated from the submitted asymmetric unit by applying the (0 0 1) translation using fractional coordinates.
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 112 / Occupancy sum non hydrogen: 175 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→10 Å
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Refine LS restraints |
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