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- PDB-1r63: STRUCTURAL ROLE OF A BURIED SALT BRIDGE IN THE 434 REPRESSOR DNA-... -

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Basic information

Entry
Database: PDB / ID: 1r63
TitleSTRUCTURAL ROLE OF A BURIED SALT BRIDGE IN THE 434 REPRESSOR DNA-BINDING DOMAIN, NMR, 20 STRUCTURES
ComponentsREPRESSOR PROTEIN FROM BACTERIOPHAGE 434
KeywordsGENE REGULATING PROTEIN / PHAGE 434 REPRESSOR / HELIX-TURN-HELIX / DNA-BINDING DOMAIN
Function / homology
Function and homology information


Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / 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 / DISTANCE GEOMETRY WITH DIANA, ENERGY MINIMIZATION WITH OPAL
AuthorsPervushin, K.V. / Billeter, M. / Siegal, G. / Wuthrich, K.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Structural role of a buried salt bridge in the 434 repressor DNA-binding domain.
Authors: Pervushin, K. / Billeter, M. / Siegal, G. / Wuthrich, K.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Determination of the Nuclear Magnetic Resonance Solution Structure of the DNA-Binding Domain (Residues 1 to 69) of the 434 Repressor and Comparison with the X-Ray Crystal Structure
Authors: Neri, D. / Billeter, M. / Wuthrich, K.
#2: Journal: J.Mol.Biol. / Year: 1989
Title: Structure of the Amino-Terminal Domain of Phage 434 Repressor at 2.0 A Resolution
Authors: Mondragon, A. / Subbiah, S. / Almo, S.C. / Drottar, M. / Harrison, S.C.
History
DepositionNov 8, 1996Processing site: BNL
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
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: REPRESSOR PROTEIN FROM BACTERIOPHAGE 434


Theoretical massNumber of molelcules
Total (without water)6,9011
Polymers6,9011
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)20 / 20DIANA PENALTY FUNCTION
Representative

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Components

#1: Protein REPRESSOR PROTEIN FROM BACTERIOPHAGE 434


Mass: 6900.871 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN, RESIDUES 1 - 63
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phage 434 (virus) / Genus: Lambda-like viruses / Species: Enterobacteria phage lambda / Production host: Escherichia coli (E. coli) / References: UniProt: P16117

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-RESOLVED NOESY
121HOMONUCLEAR NOESY
131E.COSY

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Sample preparation

Sample conditionspH: 4.8 / Temperature: 286 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
OPALLUGINBUHL,GUNTERT,BILLETER,WUTHRICHrefinement
BRUKER UXNMRUXNMRstructure solution
PROSAstructure solution
DIANAstructure solution
OPALstructure solution
RefinementMethod: DISTANCE GEOMETRY WITH DIANA, ENERGY MINIMIZATION WITH OPAL
Software ordinal: 1
NMR ensembleConformer selection criteria: DIANA PENALTY FUNCTION / Conformers calculated total number: 20 / Conformers submitted total number: 20

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