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- PDB-1j30: The crystal structure of sulerythrin, a rubrerythrin-like protein... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1j30 | ||||||
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Title | The crystal structure of sulerythrin, a rubrerythrin-like protein from a strictly aerobic and thermoacidiphilic archaeon | ||||||
![]() | 144aa long hypothetical rubrerythrin | ||||||
![]() | ELECTRON TRANSPORT / rubrerythrin / sulerythrin / Sulfolobus tokodaii strain 7 / four-helix bundle / domain swapping / metal binding site plasticity / STRUCTURAL GENOMICS | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fushinobu, S. / Shoun, H. / Wakagi, T. | ||||||
![]() | ![]() Title: The Crystal Structure of Sulerythrin, A Rubrerythrin-like Protein from A Strictly Aerobic Archaeon, Sulfolobus tokodaii strain 7, shows unexpected domain swapping Authors: Fushinobu, S. / Shoun, H. / Wakagi, T. #1: ![]() Title: Sulerythrin, the smallest member of the rubrerythrin family, from a strictly aerobic and thermoacidophilic archaeon, Sulfolobus tokodaii strain 7 Authors: Wakagi, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.7 KB | Display | ![]() |
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PDB format | ![]() | 56.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.1 KB | Display | ![]() |
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Full document | ![]() | 446.8 KB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 24.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1rytS 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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Unit cell |
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Details | The biological assembly is the dimer in the asymmetric unit. |
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Components
#1: Protein | Mass: 16098.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.41 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: ammonium sulfate, HEPES-NaOH, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 23, 2000 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→24.25 Å / Num. all: 32087 / Num. obs: 32087 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4410 / % possible all: 99.3 |
Reflection | *PLUS Num. measured all: 171729 |
Reflection shell | *PLUS % possible obs: 99.3 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1RYT Resolution: 1.7→24.29 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1564993.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: the oxygen molecules are putative. We still don't have any spectroscopic evidence to confirm that the molecule is "dioxygen".
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.4439 Å2 / ksol: 0.407613 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→24.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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