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- PDB-2l15: Solution Structure of Cold Shock Protein CspA Using Combined NMR ... -

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Basic information

Entry
Database: PDB / ID: 2l15
TitleSolution Structure of Cold Shock Protein CspA Using Combined NMR and CS-Rosetta method
ComponentsCold shock protein CspACold shock response
KeywordsTRANSCRIPTION / CspA / CS-Rosetta
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 / single-stranded RNA binding / nucleic acid binding / positive regulation of DNA-templated transcription / DNA binding / RNA binding ...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 / single-stranded RNA binding / nucleic acid binding / positive regulation of DNA-templated transcription / DNA binding / RNA binding / cytosol / cytoplasm
Similarity search - Function
Cold shock, CspA / Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock (CSD) domain profile. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold shock domain / Cold shock protein domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...Cold shock, CspA / Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock (CSD) domain profile. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / 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 / Cold shock protein CspA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsTang, Y. / Schneider, W.M. / Shen, Y. / Raman, S. / Inouye, M. / Baker, D. / Roth, M.J. / Montelione, G.T.
CitationJournal: J Struct Funct Genomics / Year: 2010
Title: Fully automated high-quality NMR structure determination of small (2)H-enriched proteins.
Authors: Tang, Y. / Schneider, W.M. / Shen, Y. / Raman, S. / Inouye, M. / Baker, D. / Roth, M.J. / Montelione, G.T.
History
DepositionJul 22, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cold shock protein CspA


Theoretical massNumber of molelcules
Total (without water)7,4111
Polymers7,4111
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)10 / 10000structures with the best score calculted by CS-Rosetta
RepresentativeModel #1lowest energy

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Components

#1: Protein Cold shock protein CspA / Cold shock response


Mass: 7411.253 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ECP_3659 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0TBP6, UniProt: P0A9X9*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HN(CA)CO
1413D HNCA
1513D HN(CO)CA
1613D HN(CA)CB
1713D HN(COCA)CB

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Sample preparation

DetailsContents: 0.2 mM [U-100% 2H; 100% 13C; U-100% 15N] ILV Methyl 1H CspA-1, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
SampleConc.: 0.2 mM / Component: CspA-1
Isotopic labeling: [U-100% 2H; 100% 13C; U-100% 15N] ILV Methyl 1H
Sample conditionsIonic strength: 50 / pH: 6.0 / Pressure: ambient / Temperature: 20 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
SPARKYGoddard and Knellerdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PSVSBhattacharya, Tejero and Montelionedata analysis
CS-RosettaBax and Yangstructure solution
CS-RosettaBax and Yangrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the best score calculted by CS-Rosetta
Conformers calculated total number: 10000 / Conformers submitted total number: 10

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