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- PDB-1aoy: N-TERMINAL DOMAIN OF ESCHERICHIA COLI ARGININE REPRESSOR NMR, 23 ... -

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Basic information

Entry
Database: PDB / ID: 1aoy
TitleN-TERMINAL DOMAIN OF ESCHERICHIA COLI ARGININE REPRESSOR NMR, 23 STRUCTURES
ComponentsARGININE REPRESSOR
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / EXPRESSION REGULATION / DNA ORGANIZATION / WINGED HELIX
Function / homology
Function and homology information


regulation of arginine biosynthetic process / regulation of arginine catabolic process / plasmid recombination / negative regulation of DNA-templated transcription initiation / positive regulation of DNA-templated transcription initiation / arginine biosynthetic process / arginine binding / cis-regulatory region sequence-specific DNA binding / protein complex oligomerization / transcription regulator complex ...regulation of arginine biosynthetic process / regulation of arginine catabolic process / plasmid recombination / negative regulation of DNA-templated transcription initiation / positive regulation of DNA-templated transcription initiation / arginine biosynthetic process / arginine binding / cis-regulatory region sequence-specific DNA binding / protein complex oligomerization / transcription regulator complex / DNA-binding transcription factor activity / identical protein binding / cytoplasm
Similarity search - Function
Arginine repressor / Arginine repressor, C-terminal / Arginine repressor, DNA-binding domain / Arginine repressor, C-terminal domain superfamily / Arginine repressor, DNA binding domain / Arginine repressor, C-terminal domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...Arginine repressor / Arginine repressor, C-terminal / Arginine repressor, DNA-binding domain / Arginine repressor, C-terminal domain superfamily / Arginine repressor, DNA binding domain / Arginine repressor, C-terminal domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsSunnerhagen, M. / Nilges, M. / Otting, G.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: Solution structure of the DNA-binding domain and model for the complex of multifunctional hexameric arginine repressor with DNA.
Authors: Sunnerhagen, M. / Nilges, M. / Otting, G. / Carey, J.
History
DepositionJul 14, 1997Processing site: BNL
Revision 1.0Sep 17, 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 1.3Apr 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ARGININE REPRESSOR


Theoretical massNumber of molelcules
Total (without water)8,7221
Polymers8,7221
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)23 / 75LOWEST ENERGY
Representative

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Components

#1: Protein ARGININE REPRESSOR


Mass: 8722.121 Da / Num. of mol.: 1 / Fragment: N-TERMINAL
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Cell line: BL21 / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): X90 (DE3) AND BL21 (DE3) ARG / Variant (production host): T7 / References: UniProt: P0A6D0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112QF-COSY
1213QF-COSY
131E-COSY
141CLEAN TOCSY
151NOESY
161HNHB
17113C-HMBC
181TOCSY-15N-HSQC
191NOESY-15N-HSQC
11013D HNCO

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Sample preparation

Sample conditionspH: 5.8 / Temperature: 301 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DMX600 / Manufacturer: Bruker / Model: DMX600 / Field strength: 600 MHz

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameVersionDeveloperClassification
X-PLOR (MODIFIED)(MODIFIED)BRUNGER (MODIFICATIONS: NILGES)refinement
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: STRUCTURES WERE CALCULATED WITH A MODIFIED VERSION OF X-PLOR WITH A SIMULATED ANNEALING PROTOCOL. AN AUTOMATED PROCEDURE (ARIA) WAS USED TO AUTOMATICALLY CALIBRATE, SELECT AND ASSIGN PEAK ...Details: STRUCTURES WERE CALCULATED WITH A MODIFIED VERSION OF X-PLOR WITH A SIMULATED ANNEALING PROTOCOL. AN AUTOMATED PROCEDURE (ARIA) WAS USED TO AUTOMATICALLY CALIBRATE, SELECT AND ASSIGN PEAK LISTS FROM HOMONUCLEAR H2O AND D2O AND N15-EDITED 3D NOESY SPECTRA. 20 STRUCTURES WERE ITERATIVELY REFINED, AND THE NOE DATA RE-ASSIGNED ON THE BASIS OF THE 7 LOWEST ENERGY STRUCTURES IN EACH ITERATION. THE AUTOMATICALLY GENERATED ASSIGNMENTS WERE CHECKED MANUALLY AND CORRECTED IF NECESSARY. THE FINAL LIST OF RESTRAINTS CONTAINED 2008 UNAMBIGUOUS RESTRAINTS AND 280 AMBIGUOUS RESTRAINTS WITH MAXIMALLY 5 ASSIGNMENT POSSIBILITIES. WITH THE FINAL RESTRAINT LIST, A TOTAL OF 75 STRUCTURES WERE CALCULATED. THE 23 STRUCTURES WITH THE LOWEST TOTAL ENERGY WERE REFINED IN AN EXPLICIT SHELL OF WATER. THE STRUCTURAL STATISTICS GIVEN BELOW ARE FOR THE STRUCTURES AFTER THE REFINEMENT IN WATER. REFINEMENT DETAILS CAN BE FOUND IN THE JRNL REFERENCE ABOVE. THE 23 DEPOSITED STRUCTURES ARE IN ORDER OF RISING RESTRAINT ENERGY AFTER WATER REFINEMENT. NOES TO ALL PROCHIRAL GROUPS WERE TREATED WITH A FLOATING CHIRALITY APPROACH THAT ALLOWS EXPLICIT SWAPPING OF PROTONS AND METHYL GROUPS; THE ATOM NAMES IN THE COORDINATE ENTRY HAVE BEEN RENAMED TO BE CONSISTENT WITH STANDARD IUB/IUPAC CONVENTION.
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 75 / Conformers submitted total number: 23

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