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Yorodumi- PDB-1et6: CRYSTAL STRUCTURE OF THE SUPERANTIGEN SMEZ-2 FROM STREPTOCOCCUS P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1et6 | ||||||
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Title | CRYSTAL STRUCTURE OF THE SUPERANTIGEN SMEZ-2 FROM STREPTOCOCCUS PYOGENES | ||||||
Components | SUPERANTIGEN SMEZ-2 | ||||||
Keywords | IMMUNE SYSTEM / beta grasp / OB fold / superantigen fold | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus pyogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.9 Å | ||||||
Authors | Arcus, V.L. / Proft, T. / Sigrell, J.A. / Baker, H.M. / Fraser, J.D. / Baker, E.N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Conservation and variation in superantigen structure and activity highlighted by the three-dimensional structures of two new superantigens from Streptococcus pyogenes. Authors: Arcus, V.L. / Proft, T. / Sigrell, J.A. / Baker, H.M. / Fraser, J.D. / Baker, E.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1et6.cif.gz | 96.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1et6.ent.gz | 73.8 KB | Display | PDB format |
PDBx/mmJSON format | 1et6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1et6_validation.pdf.gz | 429.8 KB | Display | wwPDB validaton report |
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Full document | 1et6_full_validation.pdf.gz | 433.5 KB | Display | |
Data in XML | 1et6_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 1et6_validation.cif.gz | 25.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/1et6 ftp://data.pdbj.org/pub/pdb/validation_reports/et/1et6 | 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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-Components
#1: Protein | Mass: 24218.125 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: 2035 / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RQQ5 #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: 2.28 Å3/Da / Density % sol: 46.05 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: PEG 5000 MME, cacodylate, sodium phosphate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 6.8 | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 23, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 121290 / Num. obs: 121290 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3 % / Rmerge(I) obs: 0.312 / Num. unique all: 3380 / % possible all: 98.5 |
Reflection | *PLUS Num. obs: 34777 / % possible obs: 97 % / Num. measured all: 227174 |
Reflection shell | *PLUS % possible obs: 89.9 % / Mean I/σ(I) obs: 4 |
-Processing
Software |
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Refinement | Resolution: 1.9→18.15 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 390805.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: protein.top
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.8857 Å2 / ksol: 0.343089 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→18.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 21.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.337 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.313 |