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Yorodumi- PDB-1poq: Solution Structure of a Superantigen from Yersinia pseudotuberculosis -
+Open data
-Basic information
Entry | Database: PDB / ID: 1poq | ||||||
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Title | Solution Structure of a Superantigen from Yersinia pseudotuberculosis | ||||||
Components | YPM | ||||||
Keywords | IMMUNE SYSTEM / Jelly roll fold | ||||||
Function / homology | Mitogen Ypm / Mitogen, Yersinia pseudotuberculosis / Mitogen Ypm superfamily / Yersinia pseudo-tuberculosis mitogen / Jelly Rolls / Sandwich / Mainly Beta / -derived mitogen Function and homology information | ||||||
Biological species | Yersinia pseudotuberculosis (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing, molecular dynamics, torsion angle dynamics | ||||||
Authors | Donadini, R. / Liew, C.W. / Kwan, A.H. / Mackay, J.P. / Fields, B.A. | ||||||
Citation | Journal: Structure / Year: 2004 Title: Crystal and Solution Structures of a Superantigen from Yersinia pseudotuberculosis Reveal a Jelly-Roll Fold. Authors: Donadini, R. / Liew, C.W. / Kwan, A.H. / Mackay, J.P. / Fields, B.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1poq.cif.gz | 705 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1poq.ent.gz | 609.6 KB | Display | PDB format |
PDBx/mmJSON format | 1poq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1poq_validation.pdf.gz | 345.7 KB | Display | wwPDB validaton report |
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Full document | 1poq_full_validation.pdf.gz | 534.3 KB | Display | |
Data in XML | 1poq_validation.xml.gz | 43.5 KB | Display | |
Data in CIF | 1poq_validation.cif.gz | 69.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/1poq ftp://data.pdbj.org/pub/pdb/validation_reports/po/1poq | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 13110.629 Da / Num. of mol.: 1 / Fragment: YPM(residues 33-151) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Gene: ypmA / Plasmid: pMAL-p2x / Production host: Escherichia coli (E. coli) / Strain (production host): Novablue / References: UniProt: Q57221 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using standard 2D homonuclear and triple-resonance NMR spectroscopy. |
-Sample preparation
Details | Contents: 0.5mM YPM protein (33-151), 95% H2O, 5% D2O / Solvent system: 95% H2O/5% D2O |
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Sample conditions | pH: 6.5 / Pressure: ambient / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: simulated annealing, molecular dynamics, torsion angle dynamics Software ordinal: 1 Details: Final structures were based on 1934 unambiguous NOE-derived distance constraints, 139 ambiguous constraints, 135 dihedral angle restraints and 26 hydrogen bond distance restraints. | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |