+Open data
-Basic information
Entry | Database: PDB / ID: 1ts5 | ||||||
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Title | I140T MUTANT OF TOXIC SHOCK SYNDROME TOXIN-1 FROM S. AUREUS | ||||||
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: 3.1 Å | ||||||
Authors | Earhart, C.A. / Mitchell, D.T. / Murray, D.L. / Pinheiro, D.M. / Matsumura, M. / Schlievert, P.M. / Ohlendorf, D.H. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Structures of five mutants of toxic shock syndrome toxin-1 with reduced biological activity. Authors: Earhart, C.A. / Mitchell, D.T. / Murray, D.L. / Pinheiro, D.M. / Matsumura, M. / Schlievert, P.M. / Ohlendorf, D.H. #1: 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. #2: 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 | 1ts5.cif.gz | 85.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ts5.ent.gz | 65.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ts5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ts5_validation.pdf.gz | 368 KB | Display | wwPDB validaton report |
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Full document | 1ts5_full_validation.pdf.gz | 369.5 KB | Display | |
Data in XML | 1ts5_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 1ts5_validation.cif.gz | 12.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ts/1ts5 ftp://data.pdbj.org/pub/pdb/validation_reports/ts/1ts5 | HTTPS FTP |
-Related structure data
Related structure data | 1aw7C 1ts2C 1ts3C 1ts4C 1tss S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: (-0.99913, 0.01009, -0.0404), Vector: |
-Components
#1: Protein | Mass: 22091.715 Da / Num. of mol.: 2 / Mutation: I140T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Staphylococcus aureus (bacteria) / References: UniProt: P06886 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.65 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 4 / Details: pH 4 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||
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: Nov 1, 1996 |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→20 Å / Num. obs: 11213 / % possible obs: 99 % / Redundancy: 10.3 % / Rsym value: 0.132 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 3.1→3.2 Å / Redundancy: 15.2 % / Mean I/σ(I) obs: 1 / Rsym value: 0.57 / % possible all: 100 |
Reflection | *PLUS Num. obs: 115253 / Num. measured all: 11213 / Rmerge(I) obs: 0.132 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.57 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TSS 1tss Resolution: 3.1→20 Å / Data cutoff high absF: 100000000 / Data cutoff low absF: 0 / σ(F): 0 Details: BECAUSE OF RESOLUTION, RWEIGHT WAS INCREASED 5 FOLD AND TARGET SIGMAS (FOR B'S) WERE DECREASED 5 FOLD.
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Displacement parameters | Biso mean: 16.61 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.15 Å / Rfactor Rwork: 0.255 / Total num. of bins used: 20 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.255 |