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- PDB-1b4o: NMR STUDY OF SSO7D MUTANT (F31A) MINIMIZED AVERAGE STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1b4o
TitleNMR STUDY OF SSO7D MUTANT (F31A) MINIMIZED AVERAGE STRUCTURE
ComponentsENDORIBONUCLEASE P2
KeywordsDNA BINDING PROTEIN / RNASE AND DNA-BINDING PROTEIN / THERMOSTABLE RIBONUCLEASE / SULFOLOBUS SOLFATARICUS / DNA-BINDING PROTEIN
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / DNA binding
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 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. / Tortora, P. / Zetta, L.
#1: Journal: Biochemistry / Year: 1998
Title: Differential Scanning Calorimetry Study of the Thermodynamic Stability of Some Mutants of Sso7D from Sulfolobus Solfataricus
Authors: Catanzano, F. / Graziano, G. / Fusi, P. / Tortora, P. / Barone, G.
#2: 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.
History
DepositionDec 24, 1998Processing site: BNL
Revision 1.0Jan 5, 2000Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name / _struct_keywords.text / _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: ENDORIBONUCLEASE P2


Theoretical massNumber of molelcules
Total (without water)6,9581
Polymers6,9581
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)1 / 50LOWEST ENERGY TERM
Representative

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Components

#1: Protein ENDORIBONUCLEASE P2 / SSO7D


Mass: 6958.127 Da / Num. of mol.: 1 / Mutation: F31A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSE
References: UniProt: P61991, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
121GE-TOCSY
131GE-NOESY
NMR detailsText: THE MINIMIZED AVERAGE STRUCTURE WAS DETERMINED USING 22 SELECTED CONFORMERS

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Sample preparation

DetailsContents: H2O
Sample conditionspH: 4.5 / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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: 50 / Conformers submitted total number: 1

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