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- PDB-2n48: EC-NMR Structure of Escherichia coli YiaD Determined by Combining... -

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Basic information

Entry
Database: PDB / ID: 2n48
TitleEC-NMR Structure of Escherichia coli YiaD Determined by Combining Evolutionary Couplings (EC) and Sparse NMR Data. Northeast Structural Genomics Consortium target ER553
ComponentsProbable lipoprotein YiaD
KeywordsLIPID BINDING PROTEIN / EC-NMR / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / Protein Structure Initiative / PSI-Biology / Structural Genomics
Function / homology
Function and homology information


cell outer membrane / plasma membrane
Similarity search - Function
Glycine zipper domain / Glycine zipper / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / OmpA-like domain / Outer membrane protein, bacterial / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. ...Glycine zipper domain / Glycine zipper / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / OmpA-like domain / Outer membrane protein, bacterial / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / 60s Ribosomal Protein L30; Chain: A; / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable lipoprotein YiaD
Similarity search - Component
Biological speciesEscherichia coli K-12 (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 8, 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
Remark 0THIS ENTRY 2N48 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA IN 2K1S DETERMINED ...THIS ENTRY 2N48 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA IN 2K1S DETERMINED BY AUTHORS: T.A.RAMELOT,L.ZHAO,K.HAMILTON,M.MAGLAQUI,R.XIAO,J.LIU,M.C.BARAN,G.SWAPNA,T.B.ACTON,B.ROST,G.T.MONTELIONE,M.A.KENNEDY,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable lipoprotein YiaD


Theoretical massNumber of molelcules
Total (without water)16,0561
Polymers16,0561
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 / 100lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Probable lipoprotein YiaD


Mass: 16055.984 Da / Num. of mol.: 1 / Fragment: C-terminal residues 59-199
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: yiaD, b3552, JW5657 / Production host: Escherichia coli (E. coli) / References: UniProt: P37665

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: residues 59-199 of YiaD, lipoprotein, function unknown. Homolog of OmpA-like C-terminal domain.
NMR detailsText: AUTHOR USED THE EXPERIMENTAL DATA FROM ENTRY 2K1S.

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Processing

NMR software
NameDeveloperClassification
RosettaD. Bakerrefinement
EVfold-plmdata analysis
ASDPdata analysis
CYANAGuntert, P., Mumenthaler, C. and Wuthrich, K.data analysis
EC-NMRdata analysis
TALOS+data analysis
ReduceJ. Richardson and D. Richardsonrefinement
CYANAGuntert, P., Mumenthaler, C. and Wuthrich, K.structure calculation
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 / Representative conformer: 1

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