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- PDB-1uxd: Fructose repressor DNA-binding domain, NMR, 34 structures -

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Basic information

Entry
Database: PDB / ID: 1uxd
TitleFructose repressor DNA-binding domain, NMR, 34 structures
ComponentsFRUCTOSE REPRESSOR
KeywordsTRANSCRIPTION REGULATION / DNA-BINDING PROTEIN / FRUCTOSE REPRESSOR / LACI FAMILY
Function / homology
Function and homology information


response to fructose / regulation of DNA-templated transcription initiation / cis-regulatory region sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / identical protein binding
Similarity search - Function
D-fructose-responsive transcription factor / Periplasmic binding protein/LacI sugar binding domain / Periplasmic binding proteins and sugar binding domain of LacI family / LacI-type HTH domain signature. / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / lambda repressor-like DNA-binding domains / 434 Repressor (Amino-terminal Domain) ...D-fructose-responsive transcription factor / Periplasmic binding protein/LacI sugar binding domain / Periplasmic binding proteins and sugar binding domain of LacI family / LacI-type HTH domain signature. / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / lambda repressor-like DNA-binding domains / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Periplasmic binding protein-like I / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Catabolite repressor/activator
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / DISTANCE GEOMETRY SIMULATED ANNEALING
AuthorsPenin, F. / Geourjon, C. / Montserret, R. / Bockmann, A. / Lesage, A. / Yang, Y. / Bonod-Bidaud, C. / Cortay, J.C. / Negre, D. / Cozzone, A.J. / Deleage, G.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Three-dimensional structure of the DNA-binding domain of the fructose repressor from Escherichia coli by 1H and 15N NMR.
Authors: Penin, F. / Geourjon, C. / Montserret, R. / Bockmann, A. / Lesage, A. / Yang, Y.S. / Bonod-Bidaud, C. / Cortay, J.C. / Negre, D. / Cozzone, A.J. / Deleage, G.
#1: Journal: FEBS Lett. / Year: 1996
Title: Rapid Estimation of Relative Amide Proton Exchange Rates of 15 N-Labelled Proteins by a Straightforward Water Selective Noesy-Hsqc Experiment
Authors: Bockmann, A. / Penin, F. / Guittet, E.
#2: Journal: Gene / Year: 1995
Title: Overproduction, Purification and Structural Characterization of the Functional N-Terminal DNA-Binding Domain of the Fru Repressor from Escherichia Coli K-12
Authors: Scarabel, M. / Penin, F. / Bonod-Bidaud, C. / Negre, D. / Cozzone, A.J. / Cortay, J.C.
History
DepositionDec 26, 1996Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FRUCTOSE REPRESSOR


Theoretical massNumber of molelcules
Total (without water)7,3961
Polymers7,3961
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)34 / 50RMSD AND ENERGY
Representative

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Components

#1: Protein FRUCTOSE REPRESSOR / FRUR (1-57)


Mass: 7396.483 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12
Description: OVERPRODUCED IN FUSION WITH A LQHHHHHH SEQUENCE IN C-TERMINAL END (RESIDUES 58 TO 65)
Variant: K12 / Plasmid: PCB4 / Gene (production host): FRUR1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACP1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
121TOCSY
131NOESY 15N HSQC
141J-HMQC 3D-15N HMQC-TOCSY
1513D-15N NOESY HSQC

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Sample preparation

Sample conditionspH: 5.9 / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
XPLOR3.1structure solution
RefinementMethod: DISTANCE GEOMETRY SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: RMSD AND ENERGY / Conformers calculated total number: 50 / Conformers submitted total number: 34

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