[English] 日本語
Yorodumi- PDB-2tss: TOXIC SHOCK SYNDROME TOXIN-1 FROM STAPHYLOCOCCUS AUREUS: ORTHORHO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2tss | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | TOXIC SHOCK SYNDROME TOXIN-1 FROM STAPHYLOCOCCUS AUREUS: ORTHORHOMBICC222(1) CRYSTAL FORM | |||||||||
Components | TOXIC SHOCK SYNDROME TOXIN-1 | |||||||||
Keywords | TOXIN / SUPERANTIGEN | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Staphylococcus aureus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.05 Å | |||||||||
Authors | Prasad, G.S. / Radhakrishnan, R. / Mitchell, D.T. / Earhart, C.A. / Dinges, M.M. / Cook, W.J. / Schlivert, P.M. / Ohlendorf, D.H. | |||||||||
Citation | Journal: Protein Sci. / Year: 1997 Title: Refined structures of three crystal forms of toxic shock syndrome toxin-1 and of a tetramutant with reduced activity. Authors: Prasad, G.S. / Radhakrishnan, R. / Mitchell, D.T. / Earhart, C.A. / Dinges, M.M. / Cook, W.J. / Schlievert, P.M. / Ohlendorf, D.H. #1: Journal: Biochemistry / Year: 1993 Title: Structure of Toxic Shock Syndrome Toxin 1 Authors: Prasad, G.S. / Earhart, C.A. / Murray, D.L. / Novick, R.P. / Schlievert, P.M. / Ohlendorf, D.H. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2tss.cif.gz | 133.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2tss.ent.gz | 105.5 KB | Display | PDB format |
PDBx/mmJSON format | 2tss.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2tss_validation.pdf.gz | 366.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2tss_full_validation.pdf.gz | 369.7 KB | Display | |
Data in XML | 2tss_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 2tss_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ts/2tss ftp://data.pdbj.org/pub/pdb/validation_reports/ts/2tss | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
3 |
| ||||||||||||
Unit cell |
| ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
#1: Protein | Mass: 22103.770 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: P06886 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 4.5 Details: 50-100 MM CITRATE-PHOSPHATE OR ACETATE BUFFER, PH 4-5, 4-8% PEG 4000, 0.25-1M LICL, pH 4.5 PH range: 4-5 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4,18 ℃ / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Oct 1, 1992 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→20 Å / Num. obs: 56673 / % possible obs: 94 % / Redundancy: 3.8 % / Rsym value: 0.067 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.05→2.17 Å / Redundancy: 2.71 % / Mean I/σ(I) obs: 1 / Rsym value: 0.294 / % possible all: 83 |
Reflection | *PLUS Rmerge(I) obs: 0.067 |
Reflection shell | *PLUS % possible obs: 83 % / Rmerge(I) obs: 0.294 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR / Resolution: 2.05→5 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 1
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: UNRESTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.05→2.08 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.229 |