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- PDB-2a2y: NMR Structue of Sso10b2 from Sulfolobus solfataricus -

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Basic information

Entry
Database: PDB / ID: 2a2y
TitleNMR Structue of Sso10b2 from Sulfolobus solfataricus
ComponentsDNA/RNA-binding protein Alba 2
KeywordsDNA / RNA Binding Protein / hyperthermophile protein / dimer
Function / homology
Function and homology information


chromosome condensation / chromosome / double-stranded DNA binding / RNA binding / cytoplasm
Similarity search - Function
DNA/RNA-binding protein Alba / Alba-like domain / DNA/RNA-binding protein Alba-like / Alba / Alba-like domain superfamily / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA/RNA-binding protein Alba 2
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodSOLUTION NMR / Simulated annealing using cartesian, torsion angle dynamics.
AuthorsBiyani, K. / Kahsai, M.A. / Clark, A.T. / Armstrong, T.L. / Edmondson, S.P. / Shriver, J.W.
CitationJournal: Biochemistry / Year: 2005
Title: Solution structure, stability, and nucleic Acid binding of the hyperthermophile protein sso10b2.
Authors: Biyani, K. / Kahsai, M.A. / Clark, A.T. / Armstrong, T.L. / Edmondson, S.P. / Shriver, J.W.
History
DepositionJun 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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: DNA/RNA-binding protein Alba 2
B: DNA/RNA-binding protein Alba 2


Theoretical massNumber of molelcules
Total (without water)20,5122
Polymers20,5122
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 / 10010 structures with the lowest total energy including restraint terms
RepresentativeModel #1model 1 is a restrained energy minimized average structure. models 2 through 11 are the 10 best ensemble structures.

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Components

#1: Protein DNA/RNA-binding protein Alba 2


Mass: 10255.882 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: albA2 / Plasmid: pETBlue-2 / Production host: Escherichia coli (E. coli) / Strain (production host): RosettaBlue(DE3) / References: UniProt: Q97ZF4

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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
131HNHA
143T1 T1rho HSQC
1532D 1H-15N NOE
16412C-filtered C13-edited NOESY
175IPAP HSQC
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
11 mM Sso10b2, U-15N, U-13C, pH 4.8, 90% H2O, 10% D2O90% H2O/10% D2O
21 mM Sso10b2, U-15N, U-13C, pH 4.8, 99.996% D2O99.996% D2O
31 mM Sso10b2, U-15N, pH 4.8, 90% H2O, 10% D2O90% H2O/10% D2O
4hetero-labeled dimer consisting of 0.5 mM Sso10b2 U-15N, U-13C, 0.5 mM Sso10b2 unlabled pH 5.0, 99.996% D2O99.996% D2O
51 mM Sso10b2, U-15N, pH 4.8, 90% H2O, 10% D2O with alignment media consisting of 5% C12E5/hexanol (r=.87)90% H2O, 10%D2O with alignment media consisting of 5% C12E5/hexanol (r=.87)
Sample conditionsIonic strength: 0 / pH: 4.8 / Pressure: 1 atm / Temperature: 303 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 UNITYPLUSVarianUNITYPLUS8001
Varian UNITYPLUSVarianUNITYPLUS5002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVarian, Inc.collection
NMRPipe2004F. Delaglioprocessing
NMRView5.2.2B. Johnsondata analysis
ARIA1.2M. Nilgesstructure solution
TENSOR22M. Blackledgedata analysis
Xplor-NIH2.9.7G.M. Clorerefinement
RefinementMethod: Simulated annealing using cartesian, torsion angle dynamics.
Software ordinal: 1
Details: NOE assignments, distance restraint calibrations, and initial structures were made using ARIA 1.2. Final structure refinement was done using Xplor-NIH with the NOE derived distance ...Details: NOE assignments, distance restraint calibrations, and initial structures were made using ARIA 1.2. Final structure refinement was done using Xplor-NIH with the NOE derived distance restraints, 126 phi/psi dihedral angles, 48 HNHA coupling constants, 33 hydrogen bonds, 80 dipolar couplings, 57 T1/T2 relaxation ratios, and non-crystallographic dimer symmetry restraints (numbers are per monomer). Anisotropy tensors were refined simultaneously with the structure.
NMR representativeSelection criteria: model 1 is a restrained energy minimized average structure. models 2 through 11 are the 10 best ensemble structures.
NMR ensembleConformer selection criteria: 10 structures with the lowest total energy including restraint terms
Conformers calculated total number: 100 / Conformers submitted total number: 11

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