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- PDB-8rxe: NMR Solution Structure of Cold Shock Protein CspA -

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Basic information

Entry
Database: PDB / ID: 8rxe
TitleNMR Solution Structure of Cold Shock Protein CspA
ComponentsCold shock protein CspA
KeywordsSTRUCTURAL PROTEIN / Cold Shock Protein / CspA
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, OB-fold
Similarity search - Domain/homology
Cold shock protein CspA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing / torsion angle dynamics
AuthorsWanko, M. / Dambon, C. / Feller, G. / Volkov, O.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Not funded Belgium
CitationJournal: To Be Published
Title: NMR Solution Structure of Cold Shock Protein CspA
Authors: Wanko, N.M. / Damblon, C. / Feller, G. / Volkov, O.
History
DepositionFeb 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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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)7,2801
Polymers7,2801
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cold shock protein CspA / CSP-A / 7.4 kDa cold shock protein / CS7.4


Mass: 7280.057 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cspA, cspS, b3556, JW3525 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A9X9
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic13D HN(CA)CB
141isotropic13D HN(COCA)CB
151isotropic13D (H)CCH-TOCSY
161isotropic13D (H)CCH-TOCSY
171isotropic13D 1H-13C NOESY aliphatic
181isotropic23D 1H-13C NOESY aromatic
191isotropic13D 1H-15N NOESY
1101isotropic13D HBHA(CO)NH
1111isotropic22D 1H-13C HSQC aromatic
1121isotropic22D (HB)CB(CGCD)HD
1131isotropic22D (HB)CB(CGCDCE)HE

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-13C; U-15N] Cold shock protein CspA, 50 mM potassium phosphate, 100 mM potassium chloride, 0.1 mM EDTA, 90% H2O/10% D2O
Label: 15N13C / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMCold shock protein CspA[U-13C; U-15N]1
50 mMpotassium phosphatenatural abundance1
100 mMpotassium chloridenatural abundance1
0.1 mMEDTAnatural abundance1
Sample conditionsIonic strength: 0 Not defined / Label: U-13C; U-15N / pH: 6.5 / Pressure: 1 atm / Temperature: 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD7001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNpeak picking
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
Refinement
MethodSoftware ordinal
simulated annealing8
torsion angle dynamics9
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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