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- PDB-5o6f: NMR structure of cold shock protein A from Corynebacterium pseudo... -

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Basic information

Entry
Database: PDB / ID: 5o6f
TitleNMR structure of cold shock protein A from Corynebacterium pseudotuberculosis
ComponentsCold-shock protein
KeywordsDNA BINDING PROTEIN / cold shock protein / beta-barrel / DNA binding
Function / homology
Function and homology information


nucleic acid binding / DNA binding / cytoplasm
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 / Cold shock domain-containing protein
Similarity search - Component
Biological speciesCorynebacterium pseudotuberculosis (bacteria)
MethodSOLUTION NMR / semi-autometed noe assignment, simulated annealing
AuthorsCaruso, I.P. / Panwalkar, V. / Coronado, M.A. / Dingley, A.J. / Cornelio, M.L. / Willbold, D. / Arni, R.K. / Eberle, R.J.
CitationJournal: FEBS J. / Year: 2018
Title: Structure and interaction of Corynebacterium pseudotuberculosis cold shock protein A with Y-box single-stranded DNA fragment.
Authors: Caruso, I.P. / Panwalkar, V. / Coronado, M.A. / Dingley, A.J. / Cornelio, M.L. / Willbold, D. / Arni, R.K. / Eberle, R.J.
History
DepositionJun 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.4Jun 19, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cold-shock protein


Theoretical massNumber of molelcules
Total (without water)9,1301
Polymers9,1301
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer, native gel electrophoresis, monomer
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5860 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cold-shock protein


Mass: 9129.919 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium pseudotuberculosis (bacteria)
Gene: cspA, Cp29156_0227, CpMEX31_0248 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1L6CY17, UniProt: D9QDZ8*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic23D 1H-13C NOESY
121anisotropic23D 1H-15N NOESY
131anisotropic23D 1H-13C NOESY aromatic
141anisotropic13D HNCA
151anisotropic13D HNCO
161anisotropic13D CC(CO)NH
171anisotropic13D H(CCO)NH
181anisotropic13D (H)CCH-COSY
191anisotropic12D 1H-15N HSQC
1101anisotropic12D 1H-13C HSQC
1111anisotropic12D (HB)CB(CGCD)HD
1121anisotropic12D (HB)CB(CGCDCE)HE

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Sample preparation

DetailsType: solution
Contents: 0.8 mM [U-99% 13C; U-99% 15N] Cold shock protein A, 50 mM potassium phosphate, 50 mM sodium chloride, 0.1 % sodium azide, 1 mM DSS, 93% H2O/7% D2O
Details: 50 mM potassium phosphate, 50 mM NaCl, 0.1% (w/v) NaN3, 1 mM DSS, 0.8 mM [U-99% 13C; U-99% 15N] Corynebacterium pseudotuberculosis cold shock protein A, 93% H2O/7% D2O
Label: [13C,15N]Cp-CspA / Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMCold shock protein A[U-99% 13C; U-99% 15N]1
50 mMpotassium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
0.1 %sodium azidenatural abundance1
1 mMDSSnatural abundance1
Sample conditionsIonic strength: 50 mM / Label: [13C,15N]Cp-CspA / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Varian INOVAVarianINOVA9002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisVranken, Boucher, Stevens, Fogh, Pajon, Llinas, Ulrich, Markley, Ionides, Lauedata analysis
ARIA2.3.1Rieping, Habeck, Bardiaux, Bernard, Malliavin, Nilgesstructure calculation
CNS1.21Brungerrefinement
RefinementMethod: semi-autometed noe assignment, simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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