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- PDB-1jic: SOLUTION NMR STRUCTURE OF RECOMBINANT SSO7D WITH RNASE ACTIVITY, ... -

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Basic information

Entry
Database: PDB / ID: 1jic
TitleSOLUTION NMR STRUCTURE OF RECOMBINANT SSO7D WITH RNASE ACTIVITY, MINIMIZED AVERAGE STRUCTURE
ComponentsSSO7D
KeywordsDNA BINDING PROTEIN / THERMOSTABLE RIBONUCLEASE / DNA-BINDING / SULFOLOBUS SOLFATARICUS / RNASE AND DNA-BINDING PROTEIN / DNA-BINDING PROTEIN
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / DNA binding / cytoplasm
Similarity search - Function
DNA-binding 7kDa protein / 7kD DNA-binding domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA-binding protein 7d / DNA-binding protein 7a
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodSOLUTION NMR / simulated annealing
AuthorsConsonni, R. / Santomo, L. / Zetta, L.
Citation
Journal: Biochemistry / Year: 1999
Title: A single-point mutation in the extreme heat- and pressure-resistant sso7d protein from sulfolobus solfataricus leads to a major rearrangement of the hydrophobic core.
Authors: Consonni, R. / Santomo, L. / Fusi, P. / Zetta, L.
#1: Journal: Proteins / Year: 1997
Title: Extreme Heat-and Pressure-Resistant 7-kDa Protein P2 from the Archaeon Sulfolobus Solfataricus is Dramatically Destabilized by a Single-Point Amino Acid Substitution
Authors: Fusi, P. / Goossens, K. / Consonni, R. / Grisa, M. / Puricelli, P. / Vecchio, G. / Vanoni, M. / Zetta, L. / Heremans, K. / Tortora, P.
#2: Journal: FEBS Lett. / Year: 1995
Title: 1H-NMR and Photo-Cidnp Spectroscopies Show a Possible Role for Trp23 and Phe31 in Nucleic Acid Binding by P2 Ribonuclease from the Archaeon Sulfolobus Solfataricus
Authors: Consonni, R. / Limiroli, R. / Molinari, H. / Fusi, P. / Grisa, M. / Vanoni, M. / Tortora, P.
History
DepositionJul 20, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other / Structure summary
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type / struct_keywords
Item: _pdbx_database_status.process_site / _struct_keywords.text
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SSO7D


Theoretical massNumber of molelcules
Total (without water)7,0341
Polymers7,0341
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 35LOWEST ENERGY TERM
Representative

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Components

#1: Protein SSO7D


Mass: 7034.224 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Cell line: BL21 / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSE / References: UniProt: P39476, UniProt: P61991*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111CLEAN TOCSY
121DQF COSY
131NOESY
NMR detailsText: THE MINIMIZED AVERAGE STRUCTURE WAS DETERMINED USING 15 SELECTED CONFORMERS

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Sample preparation

DetailsContents: H2O
Sample conditionspH: 4.5 / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Discover2.9DAUBER-OSGUTHORPErefinement
Discoverstructure solution
Felixstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY TERM / Conformers calculated total number: 35 / Conformers submitted total number: 1

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