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- PDB-3mef: MAJOR COLD-SHOCK PROTEIN FROM ESCHERICHIA COLI SOLUTION NMR STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 3mef
TitleMAJOR COLD-SHOCK PROTEIN FROM ESCHERICHIA COLI SOLUTION NMR STRUCTURE
ComponentsPROTEIN (COLD-SHOCK PROTEIN A)
KeywordsGENE REGULATION / COLD-SHOCK PROTEIN / TRANSCRIPTION REGULATION / SINGLE-STRANDED RNA/DNA BINDING / OB FOLD / GREEK-KEY TOPOLOGY / RNA CHAPERONE / AROMATIC-BASE STACKING INTERACTIONS
Function / homology
Function and homology information


negative regulation of termination of DNA-templated transcription / transcription antitermination factor activity, RNA binding / response to cold / single-stranded DNA binding / regulation of gene expression / nucleic acid binding / single-stranded RNA binding / positive regulation of DNA-templated transcription / DNA binding / RNA binding / cytosol
Similarity search - Function
Cold shock, CspA / : / Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold-shock (CSD) domain profile. / Cold shock domain / Cold shock protein domain / Nucleic acid-binding proteins ...Cold shock, CspA / : / Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold-shock (CSD) domain profile. / Cold shock domain / Cold shock protein domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Cold shock protein CspA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / CONSTRAINT-VIOLATION MINIMIZATION IN DIHEDRAL ANGLE SPACE
AuthorsFeng, W. / Tejero, R. / Montelione, G.T.
Citation
Journal: Biochemistry / Year: 1998
Title: Solution NMR structure and backbone dynamics of the major cold-shock protein (CspA) from Escherichia coli: evidence for conformational dynamics in the single-stranded RNA-binding site.
Authors: Feng, W. / Tejero, R. / Zimmerman, D.E. / Inouye, M. / Montelione, G.T.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Solution NMR Structure of the Major Cold Shock Protein (CspA) from Escherichia Coli: Identification of a Binding Epitope for DNA
Authors: Newkirk, K. / Feng, W. / Jiang, W. / Tejero, R. / Emerson, S.D. / Inouye, M. / Montelione, G.T.
History
DepositionOct 9, 1998Deposition site: BNL / Processing site: RCSB
SupersessionOct 14, 1998ID: 1MEF
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: 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: PROTEIN (COLD-SHOCK PROTEIN A)


Theoretical massNumber of molelcules
Total (without water)7,2801
Polymers7,2801
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)16 / 500LOWEST VALUE OF TARGET FUNCTION
RepresentativeModel #1

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Components

#1: Protein PROTEIN (COLD-SHOCK PROTEIN A) / CSPA / CS7.4


Mass: 7280.057 Da / Num. of mol.: 1 / Fragment: FULL LENGTH PROTEIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: BL21(DE3) / Description: PCR-GENERATED GENE / Gene: U60035 / Plasmid: PET11-CSPA / Species (production host): Escherichia coli / Gene (production host): U60035 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A9X9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D PFG-[15N]HSQC
1213D PFG-HNCO
1313D PFG-(HA)CA(CO)NH
1413D PFG-HA(CA)(CO)NH
1513D PFG-HA(CA)NH
1613D PFG-CBCANH
1713D PFG-CBCA(CO)NH
1813D PFG- (HA)CANH
1913D PFG-HCCNH-TOCSY
11013D PFG-HCC(CO)NH-TOCSY
11112D CT PFG-[13C 2D HSQC-TOCSY
11212D 2QF-COSY
11312D NOESY
11412D TOCSY
11513D PFG-15N-EDITED NOESY
11612D HSQC-J
NMR detailsText: THE STRUCTURES WERE DETERMINED USING DOUBLE- AND TRIPLE-RESONANCE NMR SPECTROSCOPY METHODS ON UNENRICHED, 15N-ENRICHED, AND 13C,15N-ENRICHED CSPA FROM E.COLI -

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Sample preparation

Sample conditionsIonic strength: 50 MILLIMOLAR SODIUM PHOSPHATE / pH: 6 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY 500 / Manufacturer: Varian / Model: UNITY 500 / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
DIANAWUTHRICHrefinement
DIANAstructure solution
RefinementMethod: CONSTRAINT-VIOLATION MINIMIZATION IN DIHEDRAL ANGLE SPACE
Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION
NMR ensembleConformer selection criteria: LOWEST VALUE OF TARGET FUNCTION
Conformers calculated total number: 500 / Conformers submitted total number: 16

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