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- PDB-2ef7: Crystal structure of ST2348, a hypothetical protein with CBS doma... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ef7 | ||||||
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Title | Crystal structure of ST2348, a hypothetical protein with CBS domains from Sulfolobus tokodaii strain7 | ||||||
![]() | Hypothetical protein ST2348 | ||||||
![]() | OXIDOREDUCTASE / CBS-domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | CBS-domain / CBS-domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta / CBS domain protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Agari, Y. / Karthe, P. / Kumarevel, T. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Crystal structure of ST2348, a CBS domain protein, from hyperthermophilic archaeon Sulfolobus tokodaii Authors: Ragunathan, P. / Kumarevel, T. / Agari, Y. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Ponnuraj, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.1 KB | Display | ![]() |
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PDB format | ![]() | 48.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.6 KB | Display | ![]() |
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Full document | ![]() | 437.6 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 17.6 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15146.499 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 160mM ammonium chloride, 16%(w/v) polyethylene glycol 3350, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 17, 2006 | ||||||||||||
Radiation | Monochromator: Si Double Crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.1→40 Å / Num. all: 17492 / Num. obs: 17492 / % possible obs: 99.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 32.5 | ||||||||||||
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 3.89 / Num. unique all: 1682 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.1767 Å2 / ksol: 0.368075 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→39.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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