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- PDB-1j27: Crystal structure of a hypothetical protein, TT1725, from Thermus... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1j27 | ||||||
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Title | Crystal structure of a hypothetical protein, TT1725, from Thermus thermophilus HB8 at 1.7A resolution | ||||||
![]() | hypothetical protein TT1725 | ||||||
![]() | structural genomics / unknown function / hypothetical protein from Thermus thermophilus HB8 / MAD / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | TT1725-like / Protein of unknown function DUF503 / TT1725-like superfamily / Protein of unknown function (DUF503) / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Seto, A. / Shirouzu, M. / Terada, T. / Murayama, K. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Crystal structure of a hypothetical protein, TT1725, from Thermus thermophilus HB8 at 1.7 A resolution Authors: Seto, A. / Shirouzu, M. / Terada, T. / Murayama, K. / Kuramitsu, S. / Yokoyama, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 33.5 KB | Display | ![]() |
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PDB format | ![]() | 22.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 366.5 KB | Display | ![]() |
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Full document | ![]() | 368 KB | Display | |
Data in XML | ![]() | 3.5 KB | Display | |
Data in CIF | ![]() | 5.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11421.213 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.33 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 15362 / Observed criterion σ(I): 0 / Biso Wilson estimate: 11.7 Å2 |
Reflection | *PLUS Highest resolution: 1.7 Å / % possible obs: 98.7 % / Num. measured all: 71421 / Rmerge(I) obs: 0.028 |
Reflection shell | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 1.76 Å / % possible obs: 89.6 % / Rmerge(I) obs: 0.097 / Mean I/σ(I) obs: 13.8 |
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Processing
Software | Name: CNS / Version: 1.1 / Classification: refinement | |||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 65.5761 Å2 / ksol: 0.451101 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→21.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.7 Å / % reflection Rfree: 10 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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