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- PDB-2n49: EC-NMR Structure of Erwinia carotovora ECA1580 N-terminal Domain ... -

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Basic information

Entry
Database: PDB / ID: 2n49
TitleEC-NMR Structure of Erwinia carotovora ECA1580 N-terminal Domain Determined by Combining Evolutionary Couplings (EC) and Sparse NMR Data. Northeast Structural Genomics Consortium target EwR156A
ComponentsPutative cold-shock protein
KeywordsStructural Genomics / Unknown Function / cold shock protein / GFT NMR / NESGC / EC-NMR / OB fold / protein structure / PSI / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


nucleic acid binding
Similarity search - Function
Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold-shock (CSD) domain profile. / 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 SCRI1043 (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsTang, Y. / Huang, Y.J. / Hopf, T.A. / Sander, C. / Marks, D. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Nat.Methods / Year: 2015
Title: Protein structure determination by combining sparse NMR data with evolutionary couplings.
Authors: Tang, Y. / Huang, Y.J. / Hopf, T.A. / Sander, C. / Marks, D.S. / Montelione, G.T.
History
DepositionJun 17, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Aug 12, 2015Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Remark 0THIS ENTRY 2N49 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA IN 2K5N DETERMINED ...THIS ENTRY 2N49 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA IN 2K5N DETERMINED BY AUTHORS: J.L.MILLS, A.ELETSKY, Q.ZHANG, D.LEE, M.JIANG, C.CICCOSANTI, R.XIAO, J.LUI, J.K.EVERETT, G.V.T.SWAPNA, T.B.ACTON, B.ROST, G.T.MONTELIONE, T.SZYPERSKI,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG)

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Structure visualization

Structure viewerMolecule:
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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
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 / 100lowest energy
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 SCRI1043 (bacteria)
Strain: SCRI 1043 / ATCC BAA-672 / Gene: ECA1580 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6D6V0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: Author used the experimental data from entry 2K5N.

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Sample preparation

SampleConc.: 1.07 mM / Component: EwR156A-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]

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Processing

NMR software
NameDeveloperClassification
RosettaBaker, D.refinement
EVfold-plmdata analysis
ASDPdata analysis
CYANAGuntert, P., Mumenthaler, C. and Wuthrich, K.data analysis
EC-NMRdata analysis
TALOS+data analysis
ReduceRichardson, J., Richardson, D.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: Protons from the Rosetta models were removed and added back using Reduce.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: lowest energy / Conformers calculated total number: 100 / Conformers submitted total number: 20

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