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- PDB-1a63: THE NMR STRUCTURE OF THE RNA BINDING DOMAIN OF E.COLI RHO FACTOR ... -

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Basic information

Entry
Database: PDB / ID: 1a63
TitleTHE NMR STRUCTURE OF THE RNA BINDING DOMAIN OF E.COLI RHO FACTOR SUGGESTS POSSIBLE RNA-PROTEIN INTERACTIONS, 10 STRUCTURES
ComponentsRHO
KeywordsTRANSCRIPTION TERMINATION / TERMINATION / RNA BINDING DOMAIN / TRANSCRIPTION REGULATION / OB FOLD
Function / homology
Function and homology information


ATP-dependent activity, acting on RNA / DNA-templated transcription termination / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / hydrolase activity / ATP hydrolysis activity / RNA binding / ATP binding / identical protein binding / membrane / cytosol
Similarity search - Function
Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #10 / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / Transcription termination factor Rho / Rho termination factor, N-terminal / Rho termination factor, RNA-binding domain / Transcription termination factor Rho, ATP binding domain / Rho termination factor, RNA-binding domain / Rho termination factor, N-terminal domain / Rho RNA-binding domain profile. / Rho termination factor, N-terminal domain ...Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #10 / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / Transcription termination factor Rho / Rho termination factor, N-terminal / Rho termination factor, RNA-binding domain / Transcription termination factor Rho, ATP binding domain / Rho termination factor, RNA-binding domain / Rho termination factor, N-terminal domain / Rho RNA-binding domain profile. / Rho termination factor, N-terminal domain / Rho termination factor, N-terminal domain superfamily / Cold shock domain / Cold shock protein domain / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Transcription termination factor Rho / Transcription termination factor Rho
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsBriercheck, D.M. / Wood, T.C. / Allison, T.J. / Richardson, J.P. / Rule, G.S.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: The NMR structure of the RNA binding domain of E. coli rho factor suggests possible RNA-protein interactions.
Authors: Briercheck, D.M. / Wood, T.C. / Allison, T.J. / Richardson, J.P. / Rule, G.S.
#1: Journal: To be Published
Title: Crystal Structure of the RNA-Binding Domain from Transcription Termination Factor Rho
Authors: Allison, T.J. / Wood, T.C. / Briercheck, D.M. / Rastinejad, F. / Richardson, J.P. / Rule, G.S.
#2: Journal: J.Biomol.NMR / Year: 1996
Title: 1H, 15N and 13C Resonance Assignments and Secondary Structure Determination of the RNA-Binding Domain of E.Coli Rho Protein
Authors: Briercheck, D.M. / Allison, T.J. / Richardson, J.P. / Ellena, J.F. / Wood, T.C. / Rule, G.S.
History
DepositionMar 5, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.process_site / _pdbx_nmr_software.name ..._pdbx_database_status.process_site / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model
Revision 1.4Apr 10, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: RHO


Theoretical massNumber of molelcules
Total (without water)14,6351
Polymers14,6351
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 140LOWEST ENERGY
Representative

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Components

#1: Protein RHO


Mass: 14634.602 Da / Num. of mol.: 1 / Fragment: RNA BINDING DOMAIN, RESIDUES 1 - 130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Species: Escherichia coli / Strain: BL21 (DE3) / Cell line: BL21 / Plasmid: PET11A / Species (production host): Escherichia coli / Gene (production host): RHO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P03002, UniProt: P0AG30*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: NOESY TRIPLE RESONANCE

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Sample preparation

Sample conditionspH: 7 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS5001
Bruker DMXBrukerDMX6002

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
Felixstructure solution
X-PLORBRUNGERstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: STRUCTURES WERE GENERATED USING DISTANCE GEOMETRY FOLLOWED BY SIMULATED ANNEALING. THE 10 LOWEST ENERGY STRUCTURES ARE REPORTED. THE RMSD FOR ALL BACKBONE INVOLVED IN SECONDARY STRUCTURE
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 140 / Conformers submitted total number: 10

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