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- PDB-2lfi: Solution NMR structure of a MucBP domain (fragment 187-294) of th... -

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Basic information

Entry
Database: PDB / ID: 2lfi
TitleSolution NMR structure of a MucBP domain (fragment 187-294) of the protein LBA1460 from Lactobacillus acidophilus, Northeast structural genomics consortium target LaR80A
ComponentsProtein LBA1460
KeywordsMETAL BINDING PROTEIN / NESG / PSI-Biology / Protein Structure Initiative / Putative Zn binding / Structural Genomics / Northeast Structural Genomics Consortium
Function / homologyImmunoglobulin-like - #4300 / Mub B2-like domain / Muc B2-like domain / Immunoglobulin-like / Sandwich / Mainly Beta / Putative mucus binding protein
Function and homology information
Biological speciesLactobacillus acidophilus (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsFeldmann, E.A. / Ramelot, T.A. / Yang, Y. / Lee, H. / Ciccosanti, C. / Janjua, H. / Nair, R. / Acton, T.B. / Xiao, R. / Everett, J.K. ...Feldmann, E.A. / Ramelot, T.A. / Yang, Y. / Lee, H. / Ciccosanti, C. / Janjua, H. / Nair, R. / Acton, T.B. / Xiao, R. / Everett, J.K. / Prestegard, J.H. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of a MucBP domain (fragment 187-294) of the protein LBA1460 from Lactobacillus acidophilus, Northeast structural genomics consortium target LaR80A
Authors: Feldmann, E.A. / Ramelot, T.A. / Yang, Y.A. / Wang, H. / Ciccosanti, C. / Janjua, H. / Nair, R. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A.
History
DepositionJun 30, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Structure summary
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein LBA1460


Theoretical massNumber of molelcules
Total (without water)14,0001
Polymers14,0001
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 / 200
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein LBA1460


Mass: 13999.573 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus acidophilus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5FJ43*PLUS

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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 aliphatic
1312D 1H-13C HSQC aromatic
1432D 1H-15N HSQC
1532D 1H-13C HSQC
1622D 1H-13C HSQC-CT
1713D 1H-15N NOESY
1813D 1H-13C NUS NOESY aliph
1913D HNCO
11013D HN(CA)CB
11113D CBCA(CO)NH
11213D 1H-13C NOESY arom
11313D HN(CO)CA
11413D HBHA(CO)NH
11513D C(CCO)NH
11633D (H)CCH-COSY
11713D (H)CCH-TOCSY
11833D CCH-TOCSY
11934D CC-NOESY
12012D 1H-13C HSQC aromatic
12122D 1H-15N HSQC His

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 0.02 % sodium azide, 10 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
21.2 mM U-100% 15N and 5% 13C biosynthetically directed protein, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chlorid, 10 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
31.0 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 0.02 % sodium azide, 10 mM DTT, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMprotein-1[U-100% 13C; U-100% 15N]1
20 mMMES-21
100 mMsodium chloride-31
5 mMcalcium chloride-41
0.02 %sodium azide-51
10 mMDTT-61
1.2 mMprotein-7U-100% 15N and 5% 13C biosynthetically directed2
20 mMMES-82
100 mMsodium chloride-92
5 mMcalcium chloride-102
10 mMDTT-112
0.02 %sodium azide-122
1.0 mMprotein-13[U-100% 13C; U-100% 15N]3
20 mMMES-143
100 mMsodium chloride-153
5 mMcalcium chloride-163
0.02 %sodium azide-173
10 mMDTT-183
Sample conditionsIonic strength: 0.2 / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker Avance IIIBrukerAVANCE III8502

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2008Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMR6.1CVariancollection
TopSpin2.1.4Bruker Biospincollection
AutoStructure2.2.1Huang, Tejero, Powers and Montelionedata analysis
X-PLOR NIH2.25Schwieters, Kuszewski, Tjandra and Clorestructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky3.113Goddarddata analysis
PSVS1.4Bhattacharya and Montelionerefinement
PdbStat5.1(PdbStat)-Roberto Tejero and Gaetano T. Montelionestructure solution
PINE Server1Bahrami, Markley, Assadi, and Eghbalniachemical shift autoassignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: CNS water refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformers calculated total number: 200 / Conformers submitted total number: 20

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