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- PDB-5xv9: Solution Structure of Cold Shock Protein from Colwellia psychrery... -

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Basic information

Entry
Database: PDB / ID: 5xv9
TitleSolution Structure of Cold Shock Protein from Colwellia psychrerythraea
ComponentsCold-shock DNA-binding domain family protein
KeywordsRNA BINDING PROTEIN / Cold-shock protein / Psychrophile / NMR spectroscopy / solution structure
Function / homology
Function and homology information


regulation of gene expression / DNA 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 DNA-binding domain family protein
Similarity search - Component
Biological speciesColwellia psychrerythraea (bacteria)
MethodSOLUTION NMR / na
AuthorsLee, Y. / Kim, Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation of KoreaMSIP- 2016R1A2B2008543 Korea, Republic Of
Citation
Journal: Biochemistry / Year: 2018
Title: Tyr51: Key Determinant of the Low Thermostability of the Colwellia psychrerythraea Cold-Shock Protein.
Authors: Lee, Y. / Kwak, C. / Jeong, K.W. / Durai, P. / Ryu, K.S. / Kim, E.H. / Cheong, C. / Ahn, H.C. / Kim, H.J. / Kim, Y.
#1: Journal: 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.
#2: Journal: Biochemistry / Year: 2013
Title: Structural and dynamic features of cold-shock proteins of Listeria monocytogenes, a psychrophilic bacterium
Authors: Lee, J. / Jeong, K.W. / Jin, B. / Ryu, K.S. / Kim, E.H. / Ahn, J.H. / Kim, Y.
History
DepositionJun 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.id ..._citation.country / _citation.id / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,2991
Polymers7,2991
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, no assembly
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4820 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

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


Mass: 7299.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Colwellia psychrerythraea (strain 34H / ATCC BAA-681) (bacteria)
Strain: 34H / ATCC BAA-681 / Gene: CPS_0718 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q488P6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic52D 1H-15N HSQC
122isotropic52D 1H-13C HSQC
132isotropic53D HN(CA)CB
142isotropic53D CBCA(CO)NH
152isotropic53D HNCO
162isotropic53D C(CO)NH
172isotropic53D HBHA(CO)NH
182isotropic53D H(CCO)NH
192isotropic53D (H)CCH-TOCSY
1104isotropic52D 1H-1H TOCSY
1114isotropic52D 1H-1H NOESY
1121isotropic53D 1H-15N NOESY
1132isotropic53D 1H-13C NOESY aliphatic
1141isotropic52D 1H-15N HSQC-DSSE(IPAP)
1153anisotropic52D 1H-15N HSQC-DSSE(IPAP)

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution10.5 mM [U-99% 15N] Colwellia psychrerythraea Cold Shock Protein, 50 mM potassium phosphate, 100 mM potassium chloride, 0.1 mM EDTA, 2 mM DTT, 50 nM DSS, 0.5 mg/mL sodium azide, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution20.5 mM [U-99% 13C; U-99% 15N] Colwellia psychrerythraea Cold Shock Protein, 50 mM potassium phosphate, 100 mM potassium chloride, 0.1 mM EDTA, 2 mM DTT, 50 nM DSS, 0.5 mg/mL sodium azide, 90% H2O/10% D2O13C&15N_sample90% H2O/10% D2O
gel solution30.5 mM [U-99% 15N] Colwellia psychrerythraea Cold Shock Protein, 50 mM potassium phosphate, 100 mM potassium chloride, 0.1 mM EDTA, 2 mM DTT, 50 nM DSS, 0.5 mg/mL sodium azide, 90% H2O/10% D2O15N_sample_in_gel90% H2O/10% D2O15N-labeled protein soaked into 5% acrylamide gel(4.87% acrylamide, 0.13% bis-acrylamide)
solution40.5 mM Colwellia psychrerythraea Cold Shock Protein, 50 mM potassium phosphate, 100 mM potassium chloride, 0.1 mM EDTA, 2 mM DTT, 50 nM DSS, 0.5 mg/mL sodium azide, 90% H2O/10% D2ONon-label90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMColwellia psychrerythraea Cold Shock Protein[U-99% 15N]1
50 mMpotassium phosphatenatural abundance1
100 mMpotassium chloridenatural abundance1
0.1 mMEDTAnatural abundance1
2 mMDTTnatural abundance1
50 nMDSSnatural abundance1
0.5 mg/mLsodium azidenatural abundance1
0.5 mMColwellia psychrerythraea Cold Shock Protein[U-99% 13C; U-99% 15N]2
50 mMpotassium phosphatenatural abundance2
100 mMpotassium chloridenatural abundance2
0.1 mMEDTAnatural abundance2
2 mMDTTnatural abundance2
50 nMDSSnatural abundance2
0.5 mg/mLsodium azidenatural abundance2
0.5 mMColwellia psychrerythraea Cold Shock Protein[U-99% 15N]3
50 mMpotassium phosphatenatural abundance3
100 mMpotassium chloridenatural abundance3
0.1 mMEDTAnatural abundance3
2 mMDTTnatural abundance3
50 nMDSSnatural abundance3
0.5 mg/mLsodium azidenatural abundance3
0.5 mMColwellia psychrerythraea Cold Shock Proteinnatural abundance4
50 mMpotassium phosphatenatural abundance4
100 mMpotassium chloridenatural abundance4
0.1 mMEDTAnatural abundance4
2 mMDTTnatural abundance4
50 nMDSSnatural abundance4
0.5 mg/mLsodium azidenatural abundance4
Sample conditionsIonic strength: 100 mM / Label: standard / pH: 6 / Pressure: 1 atm / Temperature: 298 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
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRFAM-SPARKYLee, Tonelli and Markleychemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
PONDEROSA-C/SLee, Cornilescu, Dashti, Eghbalnia, Tonelli, Westler, Butcher, Wildman-Henzler and Markleyrefinement
RefinementMethod: na / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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