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- PDB-1xsx: NMR Structure of Sso10a, a Hyperthermophile DNA-binding Protein w... -

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Basic information

Entry
Database: PDB / ID: 1xsx
TitleNMR Structure of Sso10a, a Hyperthermophile DNA-binding Protein with an Extended Anti-parallel Coiled Coil
ComponentsSso10a
KeywordsDNA BINDING PROTEIN / winged helix-turn-helix / anti-parallel coiled coil dimer / hyperthermophile DNA-binding protein
Function / homology
Function and homology information


ArnR1-like, winged helix-turn-helix domain / Winged helix-turn-helix / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSulfolobus solfataricus (archaea)
MethodSOLUTION NMR / Simulated annealing using cartesion, torsion angle dynamics.
Model type detailsminimized average
AuthorsKahsai, M.A. / Vogler, B. / Clark, A.T. / Edmondson, S.P. / Shriver, J.W.
CitationJournal: 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
DepositionOct 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sso10a
B: Sso10a


Theoretical massNumber of molelcules
Total (without water)22,2062
Polymers22,2062
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 7510 smallest RMSD out of 13 lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Sso10a


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
1323D 12C-filtered 13C-edited NOESY
141HNHA
2532D HSQC-IPAP
1642D HSQC T1 T1rho NOE
NMR detailsText: model 1 is an energy minimized average structure. Models 2 through 11 are the 10 best ensemble structures.

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Sample preparation

Details
Solution-IDContentsSolvent system
125 mg/ml 15N,13C Sso10a, 90% H2O, 10% D2O90% H2O/10% D2O
225 mg/ml 15N,13C Sso10a, 100% D2O100% D2O
312 mg/ml 15N Sso10a, 85% H2O, 10% D20, 5% C12E5/hexanol (r=0.87)85% H2O, 10% D20, 5% C12E5/hexanol (r=0.87)
412 mg/ml 15N Sso10a, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
15.0 ambient 303 K
25.0 ambient 308 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVarian Inc.collection
NMRPipe2004F. Delaglioprocessing
NMRView5.2.2M. Johnsondata analysis
ModelFree4A. Palmerdata analysis
ARIA1.2J. Linge, M. Nilgesstructure solution
Xplor-NIH2.9.6Brunger, Clorerefinement
Xplor-NIH2.9.6Brunger, Clorestructure solution
RefinementMethod: 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 representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: 10 smallest RMSD out of 13 lowest energy
Conformers calculated total number: 75 / Conformers submitted total number: 11

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