+Open data
-Basic information
Entry | Database: PDB / ID: 5tss | ||||||
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Title | TOXIC SHOCK SYNDROME TOXIN-1: ORTHORHOMBIC P222(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 / MOLECULAR REPLACEMENT / Resolution: 2.9 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tss.cif.gz | 87 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tss.ent.gz | 67.5 KB | Display | PDB format |
PDBx/mmJSON format | 5tss.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tss_validation.pdf.gz | 370.3 KB | Display | wwPDB validaton report |
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Full document | 5tss_full_validation.pdf.gz | 379.9 KB | Display | |
Data in XML | 5tss_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 5tss_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ts/5tss ftp://data.pdbj.org/pub/pdb/validation_reports/ts/5tss | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99889, -0.02139, 0.04192), Vector: |
-Components
#1: Protein | Mass: 22103.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Cellular location: SECRETED / Strain: MN 8 / References: UniProt: P06886 #2: Water | ChemComp-HOH / | Sequence details | TSST-1 IS PRODUCED AS A PRO-PEPTIDE WITH 40 AMINO ACIDS AT ITS AMINO-TERMINUS. THE NUMBERING SCHEME ...TSST-1 IS PRODUCED AS A PRO-PEPTIDE WITH 40 AMINO ACIDS AT ITS AMINO-TERMINUS. THE NUMBERING SCHEME HERE BEGINS WITH THE FIRST RESIDUE OF THE MATURE PROTEIN. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 50 MM TRIS-MALATE BUFFER, PH 5.8-6.6, 24% PEG 4000, 0.5-1 M LICL, pH 6.5 PH range: 5.8-6.6 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion / PH range low: 6.6 / PH range high: 5.8 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Jul 1, 1992 |
Radiation | Monochromator: YES / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. obs: 185649 / % possible obs: 98 % / Redundancy: 18.6 % / Rsym value: 0.108 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.9→2.98 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 1 / Rsym value: 0.376 / % possible all: 87 |
Reflection | *PLUS Rmerge(I) obs: 0.108 |
Reflection shell | *PLUS % possible obs: 87 % / Rmerge(I) obs: 0.376 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→5 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 1 Details: THE OCCUPANCY FOR SER A 11 THROUGH PRO A 117 IS SET TO ZERO BECAUSE OF THE ABSENCE OF 2FO-FC DENSITY. THIS SEGMENT PARTICIPATES IN A CLOSE CONTACT WITH A TWO-FOLD RELATED MOLECULE. THE ...Details: THE OCCUPANCY FOR SER A 11 THROUGH PRO A 117 IS SET TO ZERO BECAUSE OF THE ABSENCE OF 2FO-FC DENSITY. THIS SEGMENT PARTICIPATES IN A CLOSE CONTACT WITH A TWO-FOLD RELATED MOLECULE. THE CONFORMATION PRESENTED IS SIMILAR TO THAT SEEN IN OTHER CRYSTAL FORMS OF TSST-1.
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Displacement parameters | Biso mean: 20 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→5 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: UNRESTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→2.98 Å / Total num. of bins used: 20
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.204 |