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- PDB-1c20: SOLUTION STRUCTURE OF THE DNA-BINDING DOMAIN FROM THE DEAD RINGER... -

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Basic information

Entry
Database: PDB / ID: 1c20
TitleSOLUTION STRUCTURE OF THE DNA-BINDING DOMAIN FROM THE DEAD RINGER PROTEIN
ComponentsDEAD RINGER PROTEIN
KeywordsDNA BINDING PROTEIN / DNA-BINDING DOMAIN / ARID / AT-RICH INTERACTION DOMAIN / DNA-BINDING PROTEIN
Function / homology
Function and homology information


regulation of female receptivity / salivary gland development / male courtship behavior / gliogenesis / embryonic pattern specification / dendrite morphogenesis / muscle organ development / anterior/posterior pattern specification / oogenesis / axon guidance ...regulation of female receptivity / salivary gland development / male courtship behavior / gliogenesis / embryonic pattern specification / dendrite morphogenesis / muscle organ development / anterior/posterior pattern specification / oogenesis / axon guidance / DNA-binding transcription factor binding / transcription cis-regulatory region binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
REKLES domain / AT-rich interactive domain-containing protein 3 / REKLES domain profile. / ARID DNA-binding domain / ARID/BRIGHT DNA binding domain / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain ...REKLES domain / AT-rich interactive domain-containing protein 3 / REKLES domain profile. / ARID DNA-binding domain / ARID/BRIGHT DNA binding domain / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / SEE PRIMARY REFERENCE
Model type detailsminimized average
AuthorsIwahara, J. / Clubb, R.T.
CitationJournal: EMBO J. / Year: 1999
Title: Solution structure of the DNA binding domain from Dead ringer, a sequence-specific AT-rich interaction domain (ARID).
Authors: Iwahara, J. / Clubb, R.T.
History
DepositionJul 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DEAD RINGER PROTEIN


Theoretical massNumber of molelcules
Total (without water)14,9831
Polymers14,9831
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)21 / 100STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY, WITH FAVORABLE NON-BOND ENERGY, AND WITH THE LEAST RESTRAINT VIOLATIONS.
RepresentativeModel #21minimized average structure

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Components

#1: Protein DEAD RINGER PROTEIN


Mass: 14983.271 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Description: THIS SEQUENCE OCCURS NATURALLY IN DROSOPHILA MELANOGASTER
Plasmid: PGEX-4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q24573

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: SEE PRIMARY REFERENCE
NMR detailsText: SEE PRIMARY REFERENCE

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Sample preparation

Details
Solution-IDContents
11.5MM DEAD RINGER U-15N; 20MM TRIS-HCL (PH 6.7); 100MM NACL; 1.5MM ZNCL2; 2MM DTT; 0.01% NAN3
21.5MM DEAD RINGER U-15N,13C; 20MM TRIS-HCL (PH 6.7); 100MM NACL; 1.5MM ZNCL2; 2MM DTT; 0.01% NAN3
Sample conditionsIonic strength: 0.10 / pH: 6.7 / Pressure: AMBIENT / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1999DELAGLIO, F.processing
NMRView4.0.3JOHNSON, B.data analysis
X-PLOR3.8BRUNGER, A.structure solution
X-PLOR3.8BRUNGER, A.refinement
RefinementMethod: SEE PRIMARY REFERENCE / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY, WITH FAVORABLE NON-BOND ENERGY, AND WITH THE LEAST RESTRAINT VIOLATIONS.
Conformers calculated total number: 100 / Conformers submitted total number: 21

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