+Open data
-Basic information
Entry | Database: PDB / ID: 1dyq | ||||||
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Title | STAPHYLOCOCCAL ENTEROTOXIN A MUTANT VACCINE | ||||||
Components | Enterotoxin type A | ||||||
Keywords | ENTEROTOXIN / STAPHYLOCOCCAL ENTEROTOXIN TYPE A / VACCINE | ||||||
Function / homology | Function and homology information MHC class II protein binding / toxin activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Krupka, H.I. / Segelke, B.W. / Rupp, B. | ||||||
Citation | Journal: Protein Sci. / Year: 2002 Title: Structural Basis for Abrogated Binding between Staphylococcal Enterotoxin a Superantigen Vaccine and Mhc-II? Authors: Krupka, H.I. / Segelke, B.W. / Ulrich, R. / Ringhofer, S. / Knapp, M. / Rupp, B. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: THERE IS A BIFURCATED SHEET IN THIS STRUCTURE. THIS SHEET REPRESENTED ... SHEET DETERMINATION METHOD: THERE IS A BIFURCATED SHEET IN THIS STRUCTURE. THIS SHEET REPRESENTED BY TWO SHEETS WHICH HAS TWO IDENTICAL STRANDS. SHEETS A AND A1 REPRESENT ONE BIFURCATED SHEET. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dyq.cif.gz | 73.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dyq.ent.gz | 53.2 KB | Display | PDB format |
PDBx/mmJSON format | 1dyq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/1dyq ftp://data.pdbj.org/pub/pdb/validation_reports/dy/1dyq | HTTPS FTP |
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-Related structure data
Related structure data | 1esfS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | BIOLOGICAL UNIT: MONOMER |
-Components
#1: Protein | Mass: 27255.547 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Description: MUTANT GENE / Gene: entA / Plasmid: PSE380 / Gene (production host): FDA196E / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM101 / References: UniProt: P0A0L2 |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Sequence details | VACCINE MUTANT L48R, Y92A, D70R |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: HANGING DROP OVER 1 ML WELL, 4 + 4 UL DROPS, WELL SOLUTION 10% PEG6K, 5% MPD IN 0.1 M HEPES PH 7.8, TEMPERATURE 4 DEG, 3-4 WEEKS. | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / pH: 7.8 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 1999 / Details: DOUBLE FOCUSSING |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→43.19 Å / Num. obs: 35972 / % possible obs: 82.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 17.5 Å2 / Rsym value: 0.061 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 4.4 / Rsym value: 0.135 / % possible all: 46.7 |
Reflection | *PLUS Num. measured all: 158285 / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS % possible obs: 37.2 % / Num. unique obs: 1143 / Num. measured obs: 2752 / Rmerge(I) obs: 0.135 / Mean I/σ(I) obs: 3.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ESF Resolution: 1.5→43.187 Å / SU B: 1.726 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.101 Details: RESIDUES GLU 9, ASP 60 AND GLU 191 ARE IN WEAK DENSITY AND SIDE CHAIN ATOMS WERE NOT REFINED.
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Displacement parameters | Biso mean: 20 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→43.187 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.191 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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