+Open data
-Basic information
Entry | Database: PDB / ID: 1an8 | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE STREPTOCOCCAL SUPERANTIGEN SPE-C | ||||||
Components | STREPTOCOCCAL PYROGENIC EXOTOXIN C | ||||||
Keywords | BACTERIAL SUPERANTIGEN / TOXIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus pyogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.4 Å | ||||||
Authors | Roussel, A. / Baker, E.N. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1997 Title: Crystal structure of the streptococcal superantigen SPE-C: dimerization and zinc binding suggest a novel mode of interaction with MHC class II molecules. Authors: Roussel, A. / Anderson, B.F. / Baker, H.M. / Fraser, J.D. / Baker, E.N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1an8.cif.gz | 55.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1an8.ent.gz | 41 KB | Display | PDB format |
PDBx/mmJSON format | 1an8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1an8_validation.pdf.gz | 425.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1an8_full_validation.pdf.gz | 428.3 KB | Display | |
Data in XML | 1an8_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 1an8_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/1an8 ftp://data.pdbj.org/pub/pdb/validation_reports/an/1an8 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 24384.285 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P13380, UniProt: Q8NKX2*PLUS |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.98 Å3/Da / Density % sol: 75.01 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 8 Details: PROTEIN WAS CRYSTALLIZED FROM 2.7 M AMMONIUM SULFATE IN 0.1 M TRIS/HCL BUFFER AT PH 8.0 | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Type: PHOTON FACTORY / Wavelength: 1 |
Detector | Type: FILM / Detector: FILM / Date: Apr 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 17866 / % possible obs: 91.6 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 34.317 Å2 / Rsym value: 0.103 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.42→2.57 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.325 / % possible all: 87.4 |
Reflection | *PLUS Num. measured all: 71127 / Rmerge(I) obs: 0.103 |
Reflection shell | *PLUS % possible obs: 87.4 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 1.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR / Resolution: 2.4→20 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: X-PLOR ALSO WAS USED. RESIDUE 3 HAS NO REPORTED DENSITY.
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: TRONRUD METHOD / Bsol: 189.6 Å2 / ksol: 0.734 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.215 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 28.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|