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- PDB-1y9x: Solution structure of Archaeon DNA-binding protein ssh10b -

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Basic information

Entry
Database: PDB / ID: 1y9x
TitleSolution structure of Archaeon DNA-binding protein ssh10b
ComponentsDNA/RNA-binding protein Alba 1
KeywordsDNA BINDING PROTEIN / DNA BINDING / ARCHAEA
Function / homology
Function and homology information


nuclease activity / chromosome condensation / chromosome / double-stranded DNA binding / Hydrolases; Acting on ester bonds / 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 1
Similarity search - Component
Biological speciesSulfolobus shibatae (archaea)
MethodSOLUTION NMR / simulated annealing
AuthorsCui, Q. / Tong, Y. / Wang, J.
CitationJournal: Biochemistry / Year: 2008
Title: A stabilizing alpha/beta-hydrophobic core greatly contributes to hyperthermostability of archaeal [P62A]Ssh10b.
Authors: Fang, X. / Cui, Q. / Tong, Y. / Feng, Y. / Shan, L. / Huang, L. / Wang, J.
History
DepositionDec 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
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 1
B: DNA/RNA-binding protein Alba 1


Theoretical massNumber of molelcules
Total (without water)21,1512
Polymers21,1512
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

#1: Protein DNA/RNA-binding protein Alba 1 / Ssh10b


Mass: 10575.405 Da / Num. of mol.: 2 / Mutation: P62A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus shibatae (archaea) / Gene: albA1, ssh10b / Plasmid: PET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P60848

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131HNHA
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1.5mM Ssh10b U-95% 13C, U-98% 15N; 20mM acetate buffer;20mM KCl; 90%H2O,10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 20mM KCl / pH: 5 / Pressure: ambient / Temperature: 310 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ,RICE,SIMONSON,WARRENstructure solution
Felix98Accelrys, San Diegodata analysis
CNS1.1BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ,RICE,SIMONSON,WARRENrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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