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- PDB-1sro: S1 RNA BINDING DOMAIN, NMR, 20 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1sro
TitleS1 RNA BINDING DOMAIN, NMR, 20 STRUCTURES
ComponentsPNPASE
KeywordsS1 RNA-BINDING DOMAIN / POLYNUCLEOTIDE PHOSPHORYLASE (PNPASE)
Function / homology
Function and homology information


bacterial degradosome / polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / cyclic-di-GMP binding / RNA catabolic process / mRNA catabolic process / RNA processing / response to heat / 3'-5'-RNA exonuclease activity / magnesium ion binding ...bacterial degradosome / polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / cyclic-di-GMP binding / RNA catabolic process / mRNA catabolic process / RNA processing / response to heat / 3'-5'-RNA exonuclease activity / magnesium ion binding / RNA binding / identical protein binding / membrane / cytosol
Similarity search - Function
Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily / Polyribonucleotide nucleotidyltransferase / Polyribonucleotide nucleotidyltransferase, RNA-binding domain / Polyribonucleotide nucleotidyltransferase, RNA binding domain / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 ...Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily / Polyribonucleotide nucleotidyltransferase / Polyribonucleotide nucleotidyltransferase, RNA-binding domain / Polyribonucleotide nucleotidyltransferase, RNA binding domain / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / Nucleic acid-binding proteins / S1 domain / K Homology domain / K homology RNA-binding domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Polyribonucleotide nucleotidyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR
AuthorsBycroft, M.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold.
Authors: Bycroft, M. / Hubbard, T.J. / Proctor, M. / Freund, S.M. / Murzin, A.G.
#1: Journal: Gene / Year: 1992
Title: Translational Initiation Factors If-1 and Eif-2 Alpha Share an RNA-Binding Motif with Prokaryotic Ribosomal Protein S1 and Polynucleotide Phosphorylase
Authors: Gribskov, M.
History
DepositionNov 27, 1996Processing site: BNL
Revision 1.0Apr 1, 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: PNPASE


Theoretical massNumber of molelcules
Total (without water)8,3811
Polymers8,3811
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 / -
Representative

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Components

#1: Protein PNPASE / POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE / POLYNUCLEOTIDE PHOSPHORYLASE


Mass: 8380.697 Da / Num. of mol.: 1 / Fragment: S1 RNA BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PGET2T
Gene (production host): S1 RNA BINDING DOMAIN FROM ESCHERICHIA COLI PNPASE
Production host: Escherichia coli (E. coli) / References: UniProt: P05055

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR softwareName: X-PLOR / Version: 3.1 / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers submitted total number: 20

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