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- PDB-2noc: Solution Structure of Putative periplasmic protein: Northest Stru... -

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Basic information

Entry
Database: PDB / ID: 2noc
TitleSolution Structure of Putative periplasmic protein: Northest Structural Genomics Target StR106
ComponentsPutative periplasmic protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / GFT NMR / StR106 / PSI-2 / 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 / Putative periplasmic protein
Function and homology information
Biological speciesSalmonella choleraesuis (bacteria)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsZhang, Q. / Liu, G. / Wang, H. / Nwosu, C. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. ...Zhang, Q. / Liu, G. / Wang, H. / Nwosu, C. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution Structure of Putative periplasmic protein: Northest Structural Genomics Target StR106
Authors: Zhang, Q. / Liu, G. / Wang, H. / Nwosu, C. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / ACTON, T.B. / Montelione, G.T. / Szyperski, T.
History
DepositionOct 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)11,0061
Polymers11,0061
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Putative periplasmic protein


Mass: 11005.612 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella choleraesuis (bacteria) / Gene: yahO / Production host: Escherichia coli (E. coli) / References: UniProt: Q57SJ8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111GFT (4,3)D HNNCABCA
121GFT (4,3)D CABCA(CO)NHN
131GFT (4,3)D HABCAB(CO)NHN
141GFT (4,3)D (H)CCH
151SIMULTANEOUS HETERONUCLEAR RESOLVED [1H,1H]-NOESY
NMR detailsText: This structure was determined using GFT techniques

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Sample preparation

DetailsContents: 1.1 mM protein, 10mM Tris, 100mM NaCl, 0.02% NaN3, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 4.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guntert, P. et al.data analysis
NMRPipe2.3Delaglio, F. et al.processing
CYANA2.1Guntert, P. et al.structure solution
CNS1.1Brunger, A.T. et al.refinement
XEASY1.3Bartels, C., Xia, T.H.data analysis
AutoStructure2.0.0Huang, Y.J.data analysis
UBNMR1Shen, Y.data analysis
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
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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