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- PDB-2mo1: Backbone 1H, 13C, and 15N Chemical Shift Assignments for cold sho... -

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Basic information

Entry
Database: PDB / ID: 2mo1
TitleBackbone 1H, 13C, and 15N Chemical Shift Assignments for cold shock protein, TaCsp with dT7
ComponentsCold-shock DNA-binding domain protein
KeywordsDNA BINDING PROTEIN / cold shock protein / thermus aquaticus / protein stability / protein binding
Function / homology
Function and homology information


DNA binding / 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 DNA-binding domain protein
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodSOLUTION NMR / distance geometry
Model detailslowest energy, model1
AuthorsJin, B. / Jeong, K.W. / Kim, Y.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Structure and flexibility of the thermophilic cold-shock protein of Thermus aquaticus.
Authors: Jin, B. / Jeong, K.W. / Kim, Y.
History
DepositionApr 17, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Data collection / Database references / Category: citation / database_2 / pdbx_nmr_spectrometer
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cold-shock DNA-binding domain protein


Theoretical massNumber of molelcules
Total (without water)7,6931
Polymers7,6931
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)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Cold-shock DNA-binding domain protein


Mass: 7692.655 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Strain: Y51MC23 / Gene: TaqDRAFT_4615 / Production host: Escherichia coli (E. coli) / References: UniProt: B7ABH3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D HN(CA)CO
1313D CBCA(CO)NH
1413D HN(CO)CA
1513D HBHA(CO)NH
1613D HNHA
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11012D 1H-15N HSQC

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Sample preparation

DetailsContents: 50 mM potassium phosphate-1, 100 mM KCl-2, 0.1 mM EDTA-3, 0.8 mM [U-99% 13C; U-99% 15N] thermus aquaticus cold shock protein-4, 0.8 mM heptathymidine-5, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMpotassium phosphate-11
100 mMKCl-21
0.1 mMEDTA-31
0.8 mMthermus aquaticus cold shock protein-4[U-99% 13C; U-99% 15N]1
0.8 mMheptathymidine-51
Sample conditionspH: 6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE5002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichchemical shift calculation
CYANArefinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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