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- PDB-2kel: Structure of the transcription regulator SvtR from the hypertherm... -

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Basic information

Entry
Database: PDB / ID: 2kel
TitleStructure of the transcription regulator SvtR from the hyperthermophilic archaeal virus SIRV1
ComponentsUncharacterized protein 56B
KeywordsTRANSCRIPTION REPRESSOR / PROTEIN / HOMODIMER / RIBBON-HELIX-HELIX
Function / homology
Function and homology information


regulation of DNA-templated transcription
Similarity search - Function
: / 56B-like, Ribbon-helix-helix / Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Ribbon-helix-helix / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Uncharacterized protein 56B
Similarity search - Component
Biological speciesSulfolobus islandicus rod-shaped virus 1
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsGuilliere, F. / Kessler, A. / Peixeiro, N. / Sezonov, G. / Prangishvili, D. / Delepierre, M. / Guijarro, J.I.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structure, function, and targets of the transcriptional regulator SvtR from the hyperthermophilic archaeal virus SIRV1.
Authors: Guilliere, F. / Peixeiro, N. / Kessler, A. / Raynal, B. / Desnoues, N. / Keller, J. / Delepierre, M. / Prangishvili, D. / Sezonov, G. / Guijarro, J.I.
History
DepositionJan 30, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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 1.3May 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: Uncharacterized protein 56B
B: Uncharacterized protein 56B


Theoretical massNumber of molelcules
Total (without water)13,2652
Polymers13,2652
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)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein 56B / SvtR protein


Mass: 6632.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus islandicus rod-shaped virus 1
Gene: 56B, gp08 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q8QL46

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
2222D 1H-1H NOESY
1333D 1H-13C NOESY
1443D DOUBLY-FILTERED 1H-13C NOESY
1553D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.6 mM svtR, 20 mM [U-2H] sodium acetate, 90% H2O/10% D2O90% H2O/10% D2O
21.2 mM svtR, 20 mM [U-2H] sodium acetate, 100% D2O100% D2O
31.5 mM [U-98% 13C; U-98% 15N] svtR, 20 mM [U-2H] sodium acetate, 88% H2O/12% D2O88% H2O/12% D2O
42.9 mM 50%[U-98% 13C; U-98% 15N]; 50% natural abundance svtR, 20 mM [U-2H] sodium acetate, 88% H2O/12% D2O88% H2O/12% D2O
51.7 mM [U-98% 15N] svtR, 20 mM [U-2H] sodium acetate, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.6 mMsvtR-11
20 mMsodium acetate-2[U-2H]1
1.2 mMsvtR-32
20 mMsodium acetate-4[U-2H]2
1.5 mMsvtR-5[U-98% 13C; U-98% 15N]3
20 mMsodium acetate-6[U-2H]3
2.9 mMsvtR-750%[U-98% 13C; U-98% 15N]; 50% natural abundance4
20 mMsodium acetate-8[U-2H]4
1.7 mMsvtR-9[U-98% 15N]5
20 mMsodium acetate-10[U-2H]5
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.00045.5ambient 298 K
20.00045.5ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.2Linge, O'Donoghue and Nilgesstructure solution
ARIA2.2Linge, O'Donoghue and Nilgesnoe assignment
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
VnmrJ2.1BVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5.2.2Johnson, One Moon Scientificdata analysis
NMRView5.2.2Johnson, One Moon Scientificchemical shift assignment
NMRView5.2.2Johnson, One Moon Scientificpeak picking
ProcheckNMR3.4Laskowski and MacArthurdata analysis
WHAT IFVrienddata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Residues 1-12 are disordered. Only coordinates for residues 11-56 are included. Structures were calculated with restraints for residues 11-56.
NMR constraintsNOE constraints total: 4072 / NOE intraresidue total count: 1075 / NOE long range total count: 453 / NOE medium range total count: 740 / NOE sequential total count: 808 / Hydrogen bond constraints total count: 54 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 60 / Protein psi angle constraints total count: 0
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0.1 Å / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.1 Å / Torsion angle constraint violation method: CNS
NMR ensemble rmsDistance rms dev: 0.0205 Å / Distance rms dev error: 0.0001 Å

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