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Yorodumi- PDB-1xsx: NMR Structure of Sso10a, a Hyperthermophile DNA-binding Protein w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xsx | ||||||
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Title | NMR Structure of Sso10a, a Hyperthermophile DNA-binding Protein with an Extended Anti-parallel Coiled Coil | ||||||
Components | Sso10a | ||||||
Keywords | DNA BINDING PROTEIN / winged helix-turn-helix / anti-parallel coiled coil dimer / hyperthermophile DNA-binding protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | SOLUTION NMR / Simulated annealing using cartesion, torsion angle dynamics. | ||||||
Model type details | minimized average | ||||||
Authors | Kahsai, M.A. / Vogler, B. / Clark, A.T. / Edmondson, S.P. / Shriver, J.W. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Solution Structure, Stability, and Flexibility of Sso10a: A Hyperthermophile Coiled-Coil DNA-Binding Protein(,). Authors: Kahsai, M.A. / Vogler, B. / Clark, A.T. / Edmondson, S.P. / Shriver, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xsx.cif.gz | 756 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xsx.ent.gz | 644.3 KB | Display | PDB format |
PDBx/mmJSON format | 1xsx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xsx_validation.pdf.gz | 368.9 KB | Display | wwPDB validaton report |
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Full document | 1xsx_full_validation.pdf.gz | 557 KB | Display | |
Data in XML | 1xsx_validation.xml.gz | 48 KB | Display | |
Data in CIF | 1xsx_validation.cif.gz | 69.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/1xsx ftp://data.pdbj.org/pub/pdb/validation_reports/xs/1xsx | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11103.207 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: sso10a / Plasmid: pETBlue-2 / Production host: Escherichia coli (E. coli) / Strain (production host): RosettaBlue(DE3)pLacI (NOVAGEN) / References: UniProt: Q5W1E8 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: model 1 is an energy minimized average structure. Models 2 through 11 are the 10 best ensemble structures. |
-Sample preparation
Details |
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Sample conditions |
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-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: Simulated annealing using cartesion, torsion angle dynamics. Software ordinal: 1 Details: NOE assignments, distance restraint calibrations, and initial structures were made using ARIA 1.2. Final structure refinemnet was done using Xplor-NIH. Restraints consisted of 1231 ...Details: NOE assignments, distance restraint calibrations, and initial structures were made using ARIA 1.2. Final structure refinemnet was done using Xplor-NIH. Restraints consisted of 1231 intrasubunit and 83 intersubunit NOE-derived distances, 144 torsion angles, 60 HNHA coupling constants, 41 H-bonds, 52 dipolar couplings, 54 T1/T2 relaxation ratios, and non-crystallographic dimer symmetry restraints. (Numbers of restraints are per monomer.) Anisotropy tensors were included as variables during refinemnet, with best fit values for the molecular alignment tensor (from RDC's) of Da=16 Hz and rhombicity=0.24, and best fit values for the diffusion anisotropy tensor (from 15N relaxation) of Dpar/Dperp=2.0 and rhombicity=0.05 (and tauC=13.7 ns). | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: 10 smallest RMSD out of 13 lowest energy Conformers calculated total number: 75 / Conformers submitted total number: 11 |