+Open data
-Basic information
Entry | Database: PDB / ID: 1ts3 | ||||||
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Title | H135A 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 / Resolution: 2 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ts3.cif.gz | 129.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ts3.ent.gz | 101.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ts3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ts3_validation.pdf.gz | 376.8 KB | Display | wwPDB validaton report |
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Full document | 1ts3_full_validation.pdf.gz | 379.3 KB | Display | |
Data in XML | 1ts3_validation.xml.gz | 12 KB | Display | |
Data in CIF | 1ts3_validation.cif.gz | 19.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ts/1ts3 ftp://data.pdbj.org/pub/pdb/validation_reports/ts/1ts3 | HTTPS FTP |
-Related structure data
Related structure data | 1aw7C 1ts2C 1ts4C 1ts5C 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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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 22036.701 Da / Num. of mol.: 3 / Mutation: H135A 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: 3.52 Å3/Da / Density % sol: 65.03 % | ||||||||||||||||||||||||||||||
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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: Aug 1, 1997 |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 63452 / % possible obs: 100 % / Redundancy: 10.6 % / Rsym value: 0.065 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 6.46 % / Mean I/σ(I) obs: 1 / Rsym value: 0.377 / % possible all: 98 |
Reflection | *PLUS Num. measured all: 672210 / Rmerge(I) obs: 0.065 |
Reflection shell | *PLUS % possible obs: 98 % / Rmerge(I) obs: 0.377 |
-Processing
Software |
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Refinement | Starting model: PDB ENTRY 1TSS 1tss Resolution: 2→20 Å / Num. reflection obs: 51454 / Data cutoff high absF: 100000000 / Data cutoff low absF: 0 / σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.03 Å / Rfactor Rwork: 0.26 / Total num. of bins used: 20 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.178 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.26 |