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- PDB-1nla: Solution Structure of Switch Arc, a Mutant with 3(10) Helices Rep... -

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Basic information

Entry
Database: PDB / ID: 1nla
TitleSolution Structure of Switch Arc, a Mutant with 3(10) Helices Replacing a Wild-Type Beta-Ribbon
ComponentsTranscriptional repressor arc
KeywordsTRANSCRIPTION / 3(10) helix / beta-ribbon / beta-sheet / structural switching
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Arc-like DNA binding domain / Arc-like DNA binding domain / Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Ribbon-helix-helix / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional repressor arc
Similarity search - Component
Biological speciesEnterobacteria phage P22 (virus)
MethodSOLUTION NMR / simulated annealing
AuthorsCordes, M.H. / Walsh, N.P. / McKnight, C.J. / Sauer, R.T.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Solution structure of Switch Arc, a mutant with 3(10) helices replacing a wild-type beta-ribbon
Authors: Cordes, M.H. / Walsh, N.P. / McKnight, C.J. / Sauer, R.T.
History
DepositionJan 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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: Transcriptional repressor arc
B: Transcriptional repressor arc


Theoretical massNumber of molelcules
Total (without water)15,4122
Polymers15,4122
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)13 / 28structures with the least restraint violations
RepresentativeModel #3closest to the average

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Components

#1: Protein Transcriptional repressor arc


Mass: 7705.826 Da / Num. of mol.: 2 / Mutation: N11L, L12N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P22 (virus) / Genus: P22-like viruses / Gene: ARC / Plasmid: pET800 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03050

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N-separated NOESY
131HNHA
141HNHB
353HSQCs (hydrogen exchange)

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Sample preparation

Details
Solution-IDContentsSolvent system
14 mM uniform 15N-labelled Arc repressor NL11/LN12 (Switch Arc)90% H2O/10% D2O
27.5 mM 10% 13C-labelled Arc repressor NL11/LN12 (Switch Arc)90% H2O, 10% D20
35 mM uniform 15N-labelled Arc repressor NL11/LN12 (Switch Arc)100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120mM phosphate 4.8 ambient 303 K
220 mM phosphate 4.8 ambient 303 K
320 mM phosphate, 150 mM KCl 4.67 ambient 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1Brukercollection
NMRPipe1.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer, Baxprocessing
NMRDraw2.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer, Baxprocessing
NMRView3.1Johnston, Blevinsdata analysis
X-PLOR3.1Brungerstructure solution
X-PLOR3.1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Experimentally derived restraints included 810 nOe distance restraints per monomer, along with 3 hydrogen bond restraints, 31 phi-angle restraints and 3 chi1-angle restraints, for a total of ...Details: Experimentally derived restraints included 810 nOe distance restraints per monomer, along with 3 hydrogen bond restraints, 31 phi-angle restraints and 3 chi1-angle restraints, for a total of 847 restraints per monomer spanning residues 5-53. Structure calculations were performed using a simulated annealing protocol designed for symmetric dimers (M. Nilges, Proteins Struct. Funct. Gen, 17, 297 (1993)). As starting points for the calculation, 28 structures were generated in which the conformation of the N-terminal region (residues 1-13) was random, and that of the remainder of the protein restrained to be similar to wild-type Arc. The use of completely random starting structures led to extremely poor convergence rates, but those calculations which did converge yielded structures similar to those obtained from calculations using non-random starting structures. Each semi-random starting structure was then annealed to a model structure using the distance, angle and hydrogen bond restraints mentioned above. Two "seed" restraints, Arg 40 HE-Phe 45 HD and Trp 14 HE3-Tyr 38 HE, were described as unambiguously intermolecular. In the wild-type Arc structure, the difference between the intra and intermolecular distances for these atoms is >10 A. Use of the seed restraints improved convergence but again did not alter the qualitative nature of the results. All other NOE distance restraints were described ambiguously using sum potentials. Hydrogen-bond restraints in alpha-helices were described as intramonomer. In the conformational search phase of the calculations, non-bonded interactions were computed only between C-alpha atoms with a van der Waals term of 0.1. 13 of 28 calculated structures were accepted with no angle violations >5 degrees and no more than two nOe violations >0.35 A. These comprise the ensemble submitted here.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 28 / Conformers submitted total number: 13

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