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Yorodumi- PDB-1j27: Crystal structure of a hypothetical protein, TT1725, from Thermus... -
+Open data
-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 | ||||||
Components | hypothetical protein TT1725Hypothesis | ||||||
Keywords | 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 Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Seto, A. / Shirouzu, M. / Terada, T. / Murayama, K. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Proteins / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j27.cif.gz | 33.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j27.ent.gz | 22.8 KB | Display | PDB format |
PDBx/mmJSON format | 1j27.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j2/1j27 ftp://data.pdbj.org/pub/pdb/validation_reports/j2/1j27 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TT1725 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: Q84BR1 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 |
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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 |
-Processing
Software | Name: CNS / Version: 1.1 / Classification: refinement | |||||||||||||||||||||||||
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Refinement | Method to determine structure: MAD / Resolution: 1.7→21.48 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1149962.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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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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