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- PDB-2k1s: Solution NMR structure of the folded C-terminal fragment of YiaD ... -

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Basic information

Entry
Database: PDB / ID: 2k1s
TitleSolution NMR structure of the folded C-terminal fragment of YiaD from Escherichia coli. Northeast Structural Genomics Consortium target ER553.
ComponentsInner membrane lipoprotein yiaD
KeywordsLIPOPROTEIN / abbababab / OmpA / alpha beta / Inner membrane / Membrane / Palmitate / Transmembrane / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
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 (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailsresidues 59-199 of YiaD, lipoprotein, function unknown. Homolog of OmpA-like C-terminal domain.
AuthorsRamelot, T.A. / Zhao, L. / Hamilton, K. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. ...Ramelot, T.A. / Zhao, L. / Hamilton, K. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / 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 folded C-terminal fragment of YiaD from Escherichia coli. Northeast Structural Genomics Consortium target ER553.
Authors: Ramelot, T.A. / Zhao, L. / Hamilton, K. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. / Montelione, G.T. / Kennedy, M.A.
History
DepositionMar 14, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inner membrane 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 / 150structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Inner membrane lipoprotein yiaD


Mass: 16055.984 Da / Num. of mol.: 1 / Fragment: C-terminal residues 79-219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yiaD, b3552, JW5657 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pMGK / 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 experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1322D 1H-13C HSQC
1413D 1H-15N NOESY
1513D 1H-13C NOESY
1633D 1H-13C NOESY
1713D HNCO
1813D HNCA
1913D HN(CO)CA
11013D HN(CA)CB
11113D CBCA(CO)NH
11213D C(CO)NH
11313D HBHA(CO)NH
11413D H(CCO)NH
11513D (H)CCH-TOCSY
11613D (H)CCH-COSY
11734D CC NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.9 mM [U-100% 13C; U-100% 15N] YiaD protein, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21.3 mM [U-5% 13C; U-100% 15N] YiaD protein, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
31.9 mM [U-100% 13C; U-100% 15N] YiaD protein, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.9 mMYiaD protein[U-100% 13C; U-100% 15N]1
20 mMMES1
100 mMsodium chloride1
5 mMcalcium chloride1
10 mMDTT1
0.02 %sodium azide1
1.3 mMYiaD protein[U-5% 13C; U-100% 15N]2
20 mMMES2
100 mMsodium chloride2
5 mMcalcium chloride2
10 mMDTT2
0.02 %sodium azide2
1.9 mMYiaD protein[U-100% 13C; U-100% 15N]3
20 mMMES3
100 mMsodium chloride3
5 mMcalcium chloride3
10 mMDTT3
0.02 %sodium azide3
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
Varian INOVAVarianINOVA6001
Bruker AvanceIIIBrukerAVANCE III8502

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipelinux9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMR6.1CVariancollection
TopSpin2.1Bruker Biospincollection
AutoStructure2.1.1Huang, Tejero, Powers and Montelionedata analysis
X-PLOR NIH2.15.0Schwieters, Kuszewski, Tjandra and Clorestructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky3.113Goddarddata analysis
PSVS1.3Bhattacharya and Montelionestructure solution
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Xplor-NIH and CNS water refinement
NMR constraintsNOE constraints total: 1114 / NOE intraresidue total count: 36 / NOE long range total count: 513 / NOE medium range total count: 357 / NOE sequential total count: 208 / Hydrogen bond constraints total count: 2 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 99 / Protein psi angle constraints total count: 99
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 150 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 3.7 ° / Maximum upper distance constraint violation: 0.19 Å
NMR ensemble rmsDistance rms dev: 0.01 Å

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