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- PDB-1x3u: Solution structure of the C-terminal transcriptional activator do... -

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Basic information

Entry
Database: PDB / ID: 1x3u
TitleSolution structure of the C-terminal transcriptional activator domain of FixJ from Sinorhizobium melilot
ComponentsTranscriptional regulatory protein fixJ
KeywordsTRANSCRIPTION / HELIX-TURN-HELIX
Function / homology
Function and homology information


nitrogen fixation / DNA-binding transcription activator activity / phosphorelay signal transduction system / protein-DNA complex / transcription cis-regulatory region binding / positive regulation of DNA-templated transcription / metal ion binding / cytoplasm
Similarity search - Function
LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulatory protein FixJ
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsKurashima-Ito, K. / Kasai, Y. / Hosono, K. / Tamura, K. / Oue, S. / Isogai, M. / Ito, Y. / Nakamura, H. / Shiro, Y.
CitationJournal: Biochemistry / Year: 2005
Title: Solution structure of the C-terminal transcriptional activator domain of FixJ from Sinorhizobium meliloti and its recognition of the fixK promoter
Authors: Kurashima-Ito, K. / Kasai, Y. / Hosono, K. / Tamura, K. / Oue, S. / Isogai, M. / Ito, Y. / Nakamura, H. / Shiro, Y.
History
DepositionMay 10, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulatory protein fixJ


Theoretical massNumber of molelcules
Total (without water)8,5811
Polymers8,5811
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Transcriptional regulatory protein fixJ


Mass: 8580.907 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Gene: fixJ / Production host: Escherichia coli (E. coli) / References: UniProt: P10958

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1mM FixJC U-15N,13C; 20mM NaHPO4-NaH2PO4 (pH 5.5), 100mM NaCl, 50mM Na2SO4; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 5.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6collection
Azara2.7Boucher, W.processing
ANSIG3.3Kraulis, P.data analysis
CNS1structure solution
CNS1refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 80 / Conformers submitted total number: 20

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