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- PDB-1sq8: a variant 434 repressor DNA binding domain devoid of hydroxyl gro... -

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Basic information

Entry
Database: PDB / ID: 1sq8
Titlea variant 434 repressor DNA binding domain devoid of hydroxyl groups, NMR, 20 STRUCTURES
Componentsdh434
KeywordsDNA BINDING PROTEIN / HELIX-turn-Helix
Function / homology
Function and homology information


Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Repressor protein CI
Similarity search - Component
Biological speciesPhage 434 (virus)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsIwai, H. / Wider, G. / Wuthrich, K.
CitationJournal: J.Biomol.Nmr / Year: 2004
Title: NMR Structure of a Variant 434 Repressor DNA-binding Domain Devoid of Hydroxyl Groups
Authors: Iwai, H. / Wider, G. / Wuthrich, K.
History
DepositionMar 18, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
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: dh434


Theoretical massNumber of molelcules
Total (without water)7,1321
Polymers7,1321
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 / 100structures with the lowest energy
Representative

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Components

#1: Protein dh434 / variant 434 repressor DNA-binding domain


Mass: 7132.325 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phage 434 (virus) / Genus: Lambda-like viruses / Species: Enterobacteria phage lambda / Plasmid: pT7-7GFC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P16117

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY

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Sample preparation

DetailsContents: 5mM dh434, unlabeled; 25mM Potassium phosphate buffer
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 4.8 / Pressure: AMBIENT / Temperature: 286 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 750 MHz

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Processing

NMR software
NameVersionClassification
DYANA1.2structure solution
OPALrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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