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- PDB-2lnu: Solution NMR Structure of the uncharacterized protein from gene l... -

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Basic information

Entry
Database: PDB / ID: 2lnu
TitleSolution NMR Structure of the uncharacterized protein from gene locus rrnAC0354 of Haloarcula marismortui, Northeast Structural Genomics Consortium Target HmR11
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown Function / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-Biology / Protein Structure Initiative
Function / homologySingle alpha-helices involved in coiled-coils or other helix-helix interfaces - #1680 / Protein of unknown function DUF1684 / Protein of unknown function (DUF1684) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / DUF1684 domain-containing protein
Function and homology information
Biological speciesHaloarcula marismortui (Halophile)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsRossi, P. / Liu, G. / Lange, O.F. / Lee, H. / Janjua, H. / Ciccosanti, C. / Wang, H. / Acton, T.B. / Xiao, R. / Everett, J.K. ...Rossi, P. / Liu, G. / Lange, O.F. / Lee, H. / Janjua, H. / Ciccosanti, C. / Wang, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples.
Authors: Lange, O.F. / Rossi, P. / Sgourakis, N.G. / Song, Y. / Lee, H.W. / Aramini, J.M. / Ertekin, A. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Baker, D.
History
DepositionJan 5, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: Database references
Revision 1.2Jul 18, 2012Group: Database references
Revision 1.3May 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)22,0911
Polymers22,0911
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein


Mass: 22090.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809 / Gene: rrnAC0354 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q5V502

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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
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D 1H-13C arom NOESY
1713D 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1822D hetnoe
1921D T1 inv.rec
11021D T2 CPMG
11122D 1H-13C HSQC highres
1123Jmod 15N TROSY
1133jmod 15N TROSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM [U-100% 13C; U-100% 15N] HmR11, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS, 95% H2O/5% D2O95% H2O/5% D2O
21.2 mM [U-5% 13C; U-100% 15N] HmR11, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS, 95% H2O/5% D2O95% H2O/5% D2O
30.75 mM [U-5% 13C; U-100% 15N] HmR11, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMHmR11-1-1[U-100% 13C; U-100% 15N]1
0.02 %NaN3-2-21
10 mMDTT-3-31
5 mMCaCL2-4-41
100 mMNaCL-5-51
1 %Proteinase Inhibitors-6-61
20 mMMES pH 6.5-7-71
10 %D2O-8-81
50 uMDSS-9-91
1.2 mMHmR11-1-10[U-5% 13C; U-100% 15N]2
0.02 %NaN3-2-112
10 mMDTT-3-122
5 mMCaCL2-4-132
100 mMNaCL-5-142
1 %Proteinase Inhibitors-6-152
20 mMMES pH 6.5-7-162
10 %D2O-8-172
50 uMDSS-9-182
0.75 mMHmR11-19[U-5% 13C; U-100% 15N]3
0.02 %NaN3-2-203
10 mMDTT-3-213
5 mMCaCL2-4-223
100 mMNaCL-5-233
1 %Proteinase Inhibitors-6-243
20 mMMES pH 6.5-7-253
10 %D2O-8-263
50 uMDSS-9-273
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
TopSpinBruker Biospincollection
VnmrJVariancollection
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
SparkyGoddarddata analysis
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PALESPALES (Zweckstetter, Bax)geometry optimization
PSVSBhattacharya, Montelionestructure validation
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: cns with rdc noe and dihedral constraints
NMR constraintsNOE constraints total: 3463
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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