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- PDB-2jna: Solution NMR Structure of Salmonella typhimurium LT2 Secreted Pro... -

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Basic information

Entry
Database: PDB / ID: 2jna
TitleSolution NMR Structure of Salmonella typhimurium LT2 Secreted Protein STM0082: Northeast Structural Genomics Consortium Target StR109
ComponentsPutative secreted proteinSecretory protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / GFT-NMR / homodimer / PSI-2 / alpha+beta / putative secreted protein / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyYdgH/BhsA/McbA-like domain / YdgH-like superfamily / YdgH/BhsA/McbA-like domain / Flavin-binding protein dodecin / Dodecin-like / Dodecin subunit-like / 2-Layer Sandwich / Alpha Beta / Secreted protein
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, explicit water bath refinement
AuthorsEletsky, A. / Parish, D. / Liu, G. / Sukumaran, D. / Jiang, M. / Cunningham, K. / Ma, L. / Xiao, R. / Rost, B. / Montelione, G.T. ...Eletsky, A. / Parish, D. / Liu, G. / Sukumaran, D. / Jiang, M. / Cunningham, K. / Ma, L. / Xiao, R. / Rost, B. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of Salmonella typhimurium LT2 Secreted Protein STM0082: Northeast Structural Genomics Consortium Target StR109
Authors: Eletsky, A. / Parish, D. / Liu, G. / Sukumaran, D. / Jiang, M. / Cunningham, K. / Ma, L. / Xiao, R. / Rost, B. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
History
DepositionDec 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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.deposit_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative secreted protein
B: Putative secreted protein


Theoretical massNumber of molelcules
Total (without water)22,7782
Polymers22,7782
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Putative secreted protein / Secretory protein


Mass: 11388.878 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: STM0082 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q7CR88

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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 ct-HSQC aliphatic
1412D 1H-13C HSQC aromatic
1512D 1H-13C ct-HSQC aromatic
1613D HNCO
171GFT (4,3)D CABCA(CO)NHN
181GFT (4,3)D HNNCABCA
191GFT (4,3)D HABCAB(CO)NHN
1101GFT (4,3)D (H)CCH-COSY aliphatic
1111GFT (4,3)D (H)CCH-COSY aromatic
11213D 1H-13C/15N simNOESY
11333D 1H-13C X-filtered NOESY
11422D 1H-13C 28ms ct-HSQC
11522D 1H-13C 56ms ct-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.38 mM [U-100% 13C, U-100% 15N] StR109 subunit, 100 mM sodium chloride, 100 mM DTT, 5 mM CaCl2, 20 mM MES, 0.02 % sodium azide, 95% H2O, 5% D2O95% H2O/5% D2O
21.8 mM [U-5% 13C, U-100% 15N] StR109 subunit, 100 mM sodium chloride, 100 mM DTT, 5 mM CaCl2, 20 mM MES, 0.02 % sodium azide, 95% H2O, 5% D2O95% H2O/5% D2O
31.2 mM [U-100% 13C, U-100% 15N] / nat. ab. mixture StR109 subunit, 100 mM sodium chloride, 100 mM DTT, 5 mM CaCl2, 20 mM MES, 0.02 % sodium azide, 95% H2O, 5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.38 mMStR109 subunit[U-100% 13C; U-100% 15N]1
100 mMsodium chloride1
100 mMDTT1
5 mMCaCl21
20 mMMES1
0.02 %sodium azide1
1.8 mMStR109 subunit[U-5% 13C; U-100% 15N]2
100 mMsodium chloride2
100 mMDTT2
5 mMCaCl22
20 mMMES2
0.02 %sodium azide2
1.2 mMStR109 subunit[U-100% 13C; U-100% 15N] / nat. ab. mixture3
100 mMsodium chloride3
100 mMDTT3
5 mMCaCl23
20 mMMES3
0.02 %sodium azide3
Sample conditionsIonic strength: 115 / pH: 6.5 / Pressure: AMBIENT / Temperature: 298.15 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
VNMR6.1CVariancollection
XEASY1.3.13Bartels, Guntert, Billeter and Wuthrichdata analysis
AutoAssign1.15.1Zimmerman, Moseley, Kulikowski, Montelionechemical shift assignment
CARA1.5.5Keller and Wuthrichdata analysis
PROSA6.0.2Guntertprocessing
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
RefinementMethod: TORSION ANGLE DYNAMICS, explicit water bath refinement
Software ordinal: 1
NMR constraintsProtein 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: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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