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- PDB-2lss: Solution structure of the R. rickettsii cold shock-like protein -

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Basic information

Entry
Database: PDB / ID: 2lss
TitleSolution structure of the R. rickettsii cold shock-like protein
ComponentsCold shock-like protein
KeywordsRNA BINDING PROTEIN / DNA BINDING PROTEIN / cold shock-like protein / CSD / Csp / oligonucleotide binding fold / OB fold
Function / homology
Function and homology information


nucleic acid binding / cytosol / 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-like protein CspA / Cold shock-like protein CspA
Similarity search - Component
Biological speciesRickettsia rickettsii (bacteria)
MethodSOLUTION NMR / AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT.
AuthorsVeldkamp, C.T. / Peterson, F.C. / Gerarden, K.P. / Fuchs, A.M. / Koch, J.M. / Mueller, M.M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Solution structure of the cold-shock-like protein from Rickettsia rickettsii.
Authors: Gerarden, K.P. / Fuchs, A.M. / Koch, J.M. / Mueller, M.M. / Graupner, D.R. / O'Rorke, J.T. / Frost, C.D. / Heinen, H.A. / Lackner, E.R. / Schoeller, S.J. / House, P.G. / Peterson, F.C. / Veldkamp, C.T.
History
DepositionMay 4, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Nov 7, 2012Group: Database references
Revision 1.3Jan 23, 2013Group: Database references
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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_software.name / _pdbx_nmr_spectrometer.model
Revision 1.5May 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

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Assembly

Deposited unit
A: Cold shock-like protein


Theoretical massNumber of molelcules
Total (without water)7,7821
Polymers7,7821
Non-polymers00
Water00
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-like protein


Mass: 7781.743 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia rickettsii (bacteria) / Strain: Sheila Smith / Gene: A1G_05630 / Plasmid: pET28a-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8GT84, UniProt: A0A0H3AYC3*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1313D 13C-separated NOESY (AROMATIC)

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Sample preparation

DetailsContents: 1.5 mM [U-100% 13C; U-100% 15N] cold shock-like protein [Rickettsia rickettsii str. 'Sheila Smith'], 20 mM sodium phosphate, 50 mM sodium chloride, 0.02 % sodium azide, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMcold shock-like protein [Rickettsia rickettsii str. 'Sheila Smith']-1[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate-21
50 mMsodium chloride-31
0.02 %sodium azide-41
Sample conditionsIonic strength: 200 / pH: 6 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIH2.9.3SCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJANDRA,N.,CLORE,G.M.refinement
TopSpin2.1Brukercollection
NMRPipe2007Delagio,F. et al.processing
XEASY1.3Eccles, C., Guntert, P., Billeter, M., Wuthrich, K.data analysis
GARANT2.1C. Bartelsdata analysis
CYANA3.1Guntert, P.structural calculation
RefinementMethod: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT.
Software ordinal: 1
Details: RR-CSP STRUCTURES ARE BASED ON A TOTAL OF 1813 NOE CONSTRAINTS (1123 INTRA, 298 SEQUENTIAL, 86 MEDIUM, 306 LONG RANGE) AND 120 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS.
NMR constraintsNOE constraints total: 1813 / NOE intraresidue total count: 1123 / NOE long range total count: 306 / NOE medium range total count: 86 / NOE sequential total count: 298 / Protein phi angle constraints total count: 60 / Protein psi angle constraints total count: 60
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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