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- PDB-2mlg: Stf76 from the Sulfolobus islandicus plasmid-virus pSSVx -

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Basic information

Entry
Database: PDB / ID: 2mlg
TitleStf76 from the Sulfolobus islandicus plasmid-virus pSSVx
ComponentsSulfolobus transcription factor 76 aminoacid protein, Stf76
KeywordsDNA BINDING PROTEIN / winged helix domain
Function / homologyPlasmid regulator, Sulfolobaceae / Sulfolobus plasmid regulatory protein / 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 / ORF81
Function and homology information
Biological speciesFuselloviridae (virus)
MethodSOLUTION NMR / MFR
Model detailsclosest to the average, model3
AuthorsFarina, B. / Russo, L. / Fattorusso, R.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Structural and functional studies of Stf76 from the Sulfolobus islandicus plasmid-virus pSSVx: a novel peculiar member of the winged helix-turn-helix transcription factor family.
Authors: Contursi, P. / Farina, B. / Pirone, L. / Fusco, S. / Russo, L. / Bartolucci, S. / Fattorusso, R. / Pedone, E.
History
DepositionFeb 27, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Database references
Revision 1.2May 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: Sulfolobus transcription factor 76 aminoacid protein, Stf76


Theoretical massNumber of molelcules
Total (without water)10,3071
Polymers10,3071
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)20 / 3000structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Sulfolobus transcription factor 76 aminoacid protein, Stf76


Mass: 10306.946 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fuselloviridae (virus)
Description: STF76 IS A PROTEIN ENCODED BY THE PLASMID/VIRUS PSSVX. PSSVX BELONGS TO FUSELLOVIRIDAE (TAXON IDENTIFIER: 10474) AND COEXIST IN THE SAME SULFOLOBUS ISLANDICUS REY15/4 HOST (TAXON IDENTIFIER: 930945)
Production host: Escherichia coli (E. coli) / References: UniProt: O05472*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CO)CA
1413D 1H-15N NOESY
1513D 1H-15N TOCSY

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Sample preparation

DetailsContents: 100-200 uM [U-100% 13C; U-100% 15N] Stf76, 20 mM sodium phosphate, 50 mM sodium chloride, 0.02 % sodium azide, 10 % D2O, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
uMStf76-1[U-100% 13C; U-100% 15N]100-2001
20 mMsodium phosphate-21
50 mMsodium chloride-31
0.02 %sodium azide-41
10 %D2O-51
Sample conditionsIonic strength: 0.05 / pH: 5.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
CARAKeller and Wuthrichchemical shift assignment
CS-ROSETTAShen, Vernon, Baker and Baxstructure solution
CS-ROSETTAShen, Vernon, Baker and Baxrefinement
RefinementMethod: MFR / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 3000 / Conformers submitted total number: 20

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