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- PDB-1ym8: crystal structure of GZZ shows up puckering of the proline ring i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ym8 | ||||||
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Title | crystal structure of GZZ shows up puckering of the proline ring in the Xaa position. | ||||||
![]() | collagen gly-4(R)hyp-4(R)hyp | ||||||
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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 / ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schumacher, M.A. / Mizuno, K. / Bachinger, H.P. | ||||||
![]() | ![]() Title: The crystal structure of the collagen-like polypeptide (glycyl-4(R)-hydroxyprolyl-4(R)-hydroxyprolyl)9 at 1.55 A resolution shows up-puckering of the proline ring in the Xaa position. Authors: Schumacher, M. / Mizuno, K. / Bachinger, H.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 42.6 KB | Display | ![]() |
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PDB format | ![]() | 38.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1k6fS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | 3 chains fold to from triple helix with 7/2 superhelix symmetry. There are two triple helices in the ASU |
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Components
#1: Protein/peptide | Mass: 2567.547 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: synthesized peptide using ABI 433A synthesizer / References: UniProt: Q80BK4*PLUS #2: Water | ChemComp-HOH / | ![]() Compound details | COMPOUND XAA RESIDUES FOR 4(R)HYP ARE UP PUCKERED. 3 CHAINS FOLD TO FROM TRIPLE HELIX WITH 7/2 ...COMPOUND XAA RESIDUES FOR 4(R)HYP ARE UP PUCKERED. 3 CHAINS FOLD TO FROM TRIPLE HELIX WITH 7/2 SUPERHELIX | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.74 Å3/Da / Density % sol: 28.2 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: peg 400, pH 7.0, 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: Jul 22, 2003 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.55→39.88 Å / Num. all: 15444 / Num. obs: 15444 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.1 Å2 / Rsym value: 0.035 |
Reflection shell | Resolution: 1.55→1.65 Å / % possible all: 99.9 |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]() Starting model: 1K6F Resolution: 1.55→39.88 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 626016.56 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.7025 Å2 / ksol: 0.379225 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.55→39.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.65 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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