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- PDB-1v4f: Crystal structures of collagen model peptides with pro-hyp-gly se... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1v4f | ||||||
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Title | Crystal structures of collagen model peptides with pro-hyp-gly sequence at 1.3A | ||||||
![]() | (collagen like peptide) x 3 | ||||||
![]() | STRUCTURAL PROTEIN / Collagen / triple-helix | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Okuyama, K. / Hongo, C. / Fukushima, R. / Wu, G. / Noguchi, K. / Tanaka, Y. / Nishino, N. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 15.5 KB | Display | ![]() |
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PDB format | ![]() | 11.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 356.2 KB | Display | ![]() |
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Full document | ![]() | 356.1 KB | Display | |
Data in XML | ![]() | 1.8 KB | Display | |
Data in CIF | ![]() | 2.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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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 2 - 7 BY (001), AND RESIDUES 1-7 BY (002), (003), (004), (005). CHAIN B: TRANSLATE RESIDUES 3 - 7 BY (001), AND RESIDUES 1-7 BY (002), (003), (004) AND RESIDUE 1-5 BY (005). CHAIN C: TRANSLATE RESIDUES 1 - 7 BY (001), (002), (003) (004), AND RESIDUES 1-6 BY (005). THIS WILL RESULT IN A MOLECULE WITH A TOTAL OF 99 RESIDUES, 33 IN EACH CHAIN. |
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Components
#1: Protein/peptide | Mass: 609.630 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This triplet is very popular in the collagen sequence. |
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#2: Protein/peptide | Mass: 665.693 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This triplet is very popular in the collagen sequence. |
#3: Protein/peptide | Mass: 649.693 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This triplet is very popular in the collagen sequence. |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.8 % |
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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: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1.26→20 Å / Num. all: 3592 / Num. obs: 3520 / % possible obs: 98 % / Observed criterion σ(I): 1 / Redundancy: 6.67 % / Rmerge(I) obs: 0.06 / Rsym value: 0.035 / Net I/σ(I): 3.3 |
Reflection shell | Resolution: 1.26→1.32 Å / Redundancy: 4.66 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.3 / Num. unique all: 419 / % possible all: 79 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: (PRO-HYP-GLY)10 structure reported in V.Nagarajan, S.Kamitori, K.Okuyama, J.Biochem. 125, 310 (1999) Resolution: 1.26→10 Å / Num. parameters: 1396 / 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. Both up- and down- puckerings were observed for ...Details: The polymer structure can be generated from the submitted asymmetric unit by applying the (0 0 1) translation using fractional coordinates. Both up- and down- puckerings were observed for proline ring at the X position of the Gly-X-Y sequence.
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 112 / Occupancy sum non hydrogen: 182 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.26→10 Å
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Refine LS restraints |
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