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- PDB-2kcm: Solution NMR structure of the N-terminal OB-domain of SO_1732 fro... -

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Basic information

Entry
Database: PDB / ID: 2kcm
TitleSolution NMR structure of the N-terminal OB-domain of SO_1732 from Shewanella oneidensis. Northeast Structural Genomics Consortium Target SoR210A.
ComponentsCold shock domain family protein
KeywordsNUCLEIC ACID BINDING PROTEIN / beta barrel / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


nucleic acid binding / membrane => GO:0016020
Similarity search - Function
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 domain family protein
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsRamelot, T.A. / Maglaqui, M. / Jiang, M. / Ciccosanti, C. / Xiao, R. / Lui, J. / Everett, J.K. / Swapna, G. / Acton, T.B. / Rost, B. ...Ramelot, T.A. / Maglaqui, M. / Jiang, M. / Ciccosanti, C. / Xiao, R. / Lui, J. / Everett, J.K. / Swapna, G. / Acton, T.B. / Rost, B. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of the N-terminal OB-domain of SO_1732 from Shewanella oneidensis. Northeast Structural Genomics Consortium Target SoR210A.
Authors: Kennedy, M.A. / Ramelot, T.A. / Ding, K. / Maglaqui, M. / Jiang, M. / Ciccosanti, C. / Xiao, R. / Lui, J. / Everett, J.K. / Swapna, G. / Acton, T.B. / Rost, B. / Montelione, G.T.
History
DepositionDec 23, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cold shock domain family protein


Theoretical massNumber of molelcules
Total (without water)8,2851
Polymers8,2851
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 / 25structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cold shock domain family protein


Mass: 8284.524 Da / Num. of mol.: 1 / Fragment: UNP residues 1-66
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_1732 / Plasmid: pET21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8EG75

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D HNCA
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D (H)CCH-TOCSY
1613D H(CCO)NH
1713D C(CO)NH
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11012D 1H-15N HSQC
11112D 1H-13C HSQC
11222D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.84 mM [U-100% 13C; U-100% 15N] OB domain-1, 20 mM MES-2, 100 mM sodium chloride-3, 10 mM DTT-4, 5 mM calcium chloride-5, 0.02 % sodium azide-6, 95% H2O/5% D2O95% H2O/5% D2O
2.85 mM [U-5% 13C; U-99% 15N] OB domain-7, 20 mM MES-8, 100 mM sodium chloride-9, 10 mM DTT-10, 5 mM calcium chloride-11, 0.02 % sodium azide-12, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.84 mMOB domain-1[U-100% 13C; U-100% 15N]1
20 mMMES-21
100 mMsodium chloride-31
10 mMDTT-41
5 mMcalcium chloride-51
0.02 %sodium azide-61
0.85 mMOB domain-7[U-5% 13C; U-99% 15N]2
20 mMMES-82
100 mMsodium chloride-92
10 mMDTT-102
5 mMcalcium chloride-112
0.02 %sodium azide-122
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance8501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
TOPSPIN2.1Bruker Biospincollection
SPARKY3.113Goddarddata analysis
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichdata analysis
PSVS1.3Bhattacharya and Montelionedata analysis
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
X-PLOR_NIH2.2.1Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: autostructure and cyana were used to automatically assign NOE crosspeaks. xplor-NIH and CNS were used to perform hydrogen bond refinement and refinement in the presence of water.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 25 / Conformers submitted total number: 20

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