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- PDB-2k5n: Solution NMR Structure of the N-Terminal Domain of Protein ECA158... -

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Basic information

Entry
Database: PDB / ID: 2k5n
TitleSolution NMR Structure of the N-Terminal Domain of Protein ECA1580 from Erwinia carotovora, Northeast Structural Genomics Consortium Target EwR156A
ComponentsPutative cold-shock protein
Keywordsstructural genomics / unknown function / GFT NMR / protein structure / PSI / NESGC / OB fold / cold shock protein / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


nucleic acid binding
Similarity search - Function
Cold-shock (CSD) domain profile. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesPectobacterium atrosepticum (bacteria)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsMills, J.L. / Eletsky, A. / Zhang, Q. / Lee, D. / Jiang, M. / Ciccosanti, C. / Xiao, R. / Lui, J. / Everett, J.K. / Swapna, G.V.T. ...Mills, J.L. / Eletsky, A. / Zhang, Q. / Lee, D. / Jiang, M. / Ciccosanti, C. / Xiao, R. / Lui, J. / Everett, J.K. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR Structure of the Putative Cold Shock Protein from Erwinia carotovora: Northeast Structural Genomics Consortium Target EwR156a
Authors: Mills, J.L. / Eletsky, A. / Zhang, Q. / Lee, D. / Jiang, M. / Ciccosanti, C. / Xiao, R. / Lui, J. / Everett, J.K. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Szyperski, T.
History
DepositionJun 30, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 7, 2012Group: Database references / Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative cold-shock protein


Theoretical massNumber of molelcules
Total (without water)8,4181
Polymers8,4181
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 Putative cold-shock protein


Mass: 8417.549 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 100% U-15N, 13C labeled sample / Source: (gene. exp.) Pectobacterium atrosepticum (bacteria) / Genus: Erwinia / Species: carotovora / Gene: ECA1580 / Plasmid: pET 21-23C / Species (production host): coli / Production host: Escherichia coli (E. coli) / References: UniProt: Q6D6V0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1414,3 D GFT HNNACBCA
1514,3 D GFT CABCACONHN
1614,3D HABCAB(CO)NHN
1714,3D GFT (H)CCH COSY
1813D (H)CCH-COSY
1913D simultaneous NOESY
11022D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.07 mM [U-100% 13C; U-100% 15N] NC, 0.02 % sodium azide, 100 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 20 mM MES, 95% H2O/5% D2O95% H2O/5% D2O
21.864 mM [U-5% 13C; U-100% 15N] NC5, 0.02 % sodium azide, 100 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 20 mM MES, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.07 mMNC[U-100% 13C; U-100% 15N]1
0.02 %sodium azide1
100 mMDTT1
5 mMcalcium chloride1
100 mMsodium chloride1
20 mMMES1
1.864 mMNC5[U-5% 13C; U-100% 15N]2
0.02 %sodium azide2
100 mMDTT2
5 mMcalcium chloride2
100 mMsodium chloride2
20 mMMES2
Sample conditionsIonic strength: 0.235 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMRJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SPSCANGlaserprocessing
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
AutoAssignZimmerman, Moseley, Kulikowski and Montelionedata analysis
TALOSCornilescu, Delaglio and Baxstructure solution
CSI(CSI) Wishart and Sykesstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructureHuang, Tejero, Powers and Montelionestructure solution
MolmolKoradi, Billeter and Wuthrichdata analysis
MolmolKoradi, Billeter and Wuthrichrefinement
PSVSBhattacharya and Montelionerefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
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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