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- PDB-1exe: SOLUTION STRUCTURE OF A MUTANT OF TRANSCRIPTION FACTOR 1. -

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Basic information

Entry
Database: PDB / ID: 1exe
TitleSOLUTION STRUCTURE OF A MUTANT OF TRANSCRIPTION FACTOR 1.
ComponentsTRANSCRIPTION FACTOR 1
KeywordsTRANSCRIPTION / beta ribbon arms / DNA-binding / DNA-bending protein
Function / homology
Function and homology information


structural constituent of chromatin / DNA binding
Similarity search - Function
HU Protein; Chain A / IHF-like DNA-binding proteins / Histone-like DNA-binding protein, conserved site / Bacterial histone-like DNA-binding proteins signature. / Histone-like DNA-binding protein / Bacterial DNA-binding protein / bacterial (prokaryotic) histone like domain / Integration host factor (IHF)-like DNA-binding domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Transcription factor 1
Similarity search - Component
Biological speciesBacillus phage SPO1 (virus)
MethodSOLUTION NMR / Distance geometry, simulated annealing, molecular dynamics
AuthorsLiu, W. / Vu, H.M. / Geiduschek, E.P. / Kearns, D.R.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Solution structure of a mutant of transcription factor 1: implications for enhanced DNA binding.
Authors: Liu, W. / Vu, H.M. / Geiduschek, E.P. / Kearns, D.R.
#1: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 2000
Title: Mechanisms for the Enhanced Thermal Stability of a Mutant of Transcription Factor 1 as Explained by 1H, 15N and 13C NMR Chemical Shifts and Secondary Structure Analysis.
Authors: Vu, H.M. / Liu, W. / Grove, A. / Geiduschek, E.P. / Kearns, D.R.
#2: Journal: J.Mol.Biol. / Year: 1996
Title: Structure of the Bacillus subtilis phage SPO1-encoded Type II DNA-binding Protein TF1 in Solution.
Authors: Jia, X. / Grove, A. / Ivancic, M. / Hsu, V.L. / Geiduschek, E.P. / Kearns, D.R.
History
DepositionMay 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: 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
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: TRANSCRIPTION FACTOR 1
B: TRANSCRIPTION FACTOR 1


Theoretical massNumber of molelcules
Total (without water)21,3852
Polymers21,3852
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)23 / 50structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein TRANSCRIPTION FACTOR 1


Mass: 10692.382 Da / Num. of mol.: 2 / Mutation: E15G;T32I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage SPO1 (virus) / Genus: SPO1-like viruses / Plasmid: PBTF1X / Production host: Escherichia coli (E. coli) / References: UniProt: P04445

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
2323D 15N-separated NOESY
3433D 13C-separated NOESY
353HNCA-J

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM TF1-G15/I32, 100 mM phosphate buffer90% H2O/10% D2O
22 mM TF1-G15/I32, U-15N, 100 mM phosphate buffer90% H2O/10% D2O
32 mM TF1-G15/I32, U-15N, 13C, 100 mM Phosphate buffer90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1400 mM NaCl 6.7Ambient 308 K
2400 mM NaCl 6.7Ambient 308 K
3400 mM NaCl 6.7Ambient 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.3Brukercollection
Felix97MSIprocessing
Felix97MSIdata analysis
X-PLOR3Brungerstructure solution
X-PLOR3Brungerrefinement
RefinementMethod: Distance geometry, simulated annealing, molecular dynamics
Software ordinal: 1
Details: The structures were based on a total of 2008 NOE-derived distance constraints, 288 dihedral angle restraints and 116 H-bond constraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 23

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