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- PDB-2ma4: Solution NMR Structure of yahO protein from Salmonella typhimuriu... -

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Basic information

Entry
Database: PDB / ID: 2ma4
TitleSolution NMR Structure of yahO protein from Salmonella typhimurium, Northeast Structural Genomics Consortium (NESG) Target StR106
ComponentsPutative periplasmic protein
KeywordsMEMBRANE PROTEIN / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / PSI-Biology / Protein Structure Initiative / DUF1471
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 / Putative periplasmic protein
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsEletsky, A. / Zhang, Q. / Liu, G. / Wang, H. / Nwosu, C. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. ...Eletsky, A. / Zhang, Q. / Liu, G. / Wang, H. / Nwosu, C. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Plos One / Year: 2014
Title: Structural and Functional Characterization of DUF1471 Domains of Salmonella Proteins SrfN, YdgH/SssB, and YahO.
Authors: Eletsky, A. / Michalska, K. / Houliston, S. / Zhang, Q. / Daily, M.D. / Xu, X. / Cui, H. / Yee, A. / Lemak, A. / Wu, B. / Garcia, M. / Burnet, M.C. / Meyer, K.M. / Aryal, U.K. / Sanchez, O. ...Authors: Eletsky, A. / Michalska, K. / Houliston, S. / Zhang, Q. / Daily, M.D. / Xu, X. / Cui, H. / Yee, A. / Lemak, A. / Wu, B. / Garcia, M. / Burnet, M.C. / Meyer, K.M. / Aryal, U.K. / Sanchez, O. / Ansong, C. / Xiao, R. / Acton, T.B. / Adkins, J.N. / Montelione, G.T. / Joachimiak, A. / Arrowsmith, C.H. / Savchenko, A. / Szyperski, T. / Cort, J.R.
History
DepositionJun 27, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Jun 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
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative periplasmic protein


Theoretical massNumber of molelcules
Total (without water)8,7451
Polymers8,7451
Non-polymers00
Water00
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 periplasmic protein


Mass: 8744.854 Da / Num. of mol.: 1 / Fragment: UNP residues 22-91
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: STM0366, STM4576, yahO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q7CR49

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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
1313D HNCO
141(4,3)D GFT CABCA(CO)NHN
151(4,3)D GFT HNHNCABCA
161(4,3)D GFT HABCAB(CO)NHN
1713D 1H-15N,13C NOESY
181(4,3)D GFT (H)CCH-COSY aliphatic
1913D (H)CCH-COSY aromatic
11013D (H)CCH-TOCSY aliphatic
11112D 1H-13C HSQC aromatic
11222D 1H-13C HSQC methyl
11332D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM [U-100% 13C; U-100% 15N] StR106, 0.02 % NaN3, 10 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 20 mM ammonium acetate, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [5% 13C; U-100% 15N] StR106, 0.02 % NaN3, 10 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 20 mM ammonium acetate, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
30.3 mM [U-100% 13C; U-100% 15N] StR106, 0.02 % NaN3, 10 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 20 mM ammonium acetate, 50 uM DSS, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMStR106-1[U-100% 13C; U-100% 15N]1
0.02 %NaN3-21
10 mMDTT-31
5 mMcalcium chloride-41
100 mMsodium chloride-51
20 mMammonium acetate-61
50 uMDSS-71
1 mMStR106-8[5% 13C; U-100% 15N]2
0.02 %NaN3-92
10 mMDTT-102
5 mMcalcium chloride-112
100 mMsodium chloride-122
20 mMammonium acetate-132
50 uMDSS-142
0.3 mMStR106-15[U-100% 13C; U-100% 15N]3
0.02 %NaN3-163
10 mMDTT-173
5 mMcalcium chloride-183
100 mMsodium chloride-193
20 mMammonium acetate-203
50 uMDSS-213
Sample conditionspH: 4.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AS-DP1Huang, Tejero, Powers and Montelionestructure calculation
AS-DP1Huang, Tejero, Powers and Montelionerefinement
XEASY1.3.13Bartels et al.data analysis
XEASY1.3.13Bartels et al.peak picking
XEASY1.3.13Bartels et al.chemical shift assignment
XEASY1.3.13Bartels et al.data analysis
XEASY1.3.13Keller and Wuthrichdata analysis
XEASY1.3.13Keller and Wuthrichpeak picking
XEASY1.3.13Keller and Wuthrichchemical shift assignment
XEASY1.3.13Keller and Wuthrichdata analysis
VnmrJ2.2DVariancollection
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PSVS1.4Bhattacharya, Montelionestructure validation
XEASY1.3.13Bartels et al.data analysis,peak picking,chemical shift assignment
XEASY1.3.13Bartels et al.data analysis
XEASY1.3.13Keller and Wuthrichdata analysis,peak picking,chemical shift assignment
XEASY1.3.13Keller and Wuthrichdata analysis
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PROSA6.4Guntertprocessing
DYANA1.5Guntert, Braun and Wuthrichdata analysis
UBNMR1Shendata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: STRUCTURE DETERMINATION WAS PERFORMED BY RUNNING CYANA AND ASDP IN PARALLEL USING NOE-BASED CONSTRAINTS AND PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS FROM TALOS+. CONSENSUS PEAK ASSIGNMENTS ...Details: STRUCTURE DETERMINATION WAS PERFORMED BY RUNNING CYANA AND ASDP IN PARALLEL USING NOE-BASED CONSTRAINTS AND PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS FROM TALOS+. CONSENSUS PEAK ASSIGNMENTS WERE SELECTED AND USED IN ITERATIVE REFINEMENT WITH CYANA. THE 20 CONFORMERS OUT OF 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY SIMULATED ANNEALING IN EXPLICIT WATER BATH USING THE PROGRAM CNS WITH PARAM19 FORCE FIELD
NMR constraintsNOE constraints total: 1664 / NOE intraresidue total count: 295 / NOE long range total count: 570 / NOE medium range total count: 370 / NOE sequential total count: 429 / Hydrogen bond constraints total count: 62 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 50 / Protein psi angle constraints total count: 50
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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