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- PDB-1puz: Solution NMR Structure of Protein NMA1147 from Neisseria meningit... -

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Basic information

Entry
Database: PDB / ID: 1puz
TitleSolution NMR Structure of Protein NMA1147 from Neisseria meningitidis. Northeast Structural Genomics Consortium Target MR19
Componentsconserved hypothetical protein
Keywordsstructural genomics / unknown function / NMA1147 / MR19 / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyFlavinator of succinate dehydrogenase / Flavinator of succinate dehydrogenase / Flavinator of succinate dehydrogenase superfamily / Flavinator of succinate dehydrogenase / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha / FAD assembly factor SdhE / :
Function and homology information
Biological speciesNeisseria meningitidis (bacteria)
MethodSOLUTION NMR / distance geometry simulated annealing torsion angle dynamics
AuthorsLiu, G. / Xu, D. / Sukumaran, D.K. / Chiang, Y. / Acton, T. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proteins / Year: 2004
Title: NMR structure of the hypothetical protein NMA1147 from Neisseria meningitidis reveals a distinct 5-helix bundle.
Authors: Liu, G. / Sukumaran, D.K. / Xu, D. / Chiang, Y. / Acton, T. / Goldsmith-Fischman, S. / Honig, B. / Montelione, G.T. / Szyperski, T.
History
DepositionJun 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: conserved hypothetical protein


Theoretical massNumber of molelcules
Total (without water)9,8101
Polymers9,8101
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 #1fewest violations

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Components

#1: Protein conserved hypothetical protein


Mass: 9810.358 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: NMA1147 OR NMB0952 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JR91, UniProt: Q7DDK1*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY
132HNHA
14213C-CT-HSQC
151HNNCAHA
161HACA(co)NHN
171HABCAB(co)NHN
NMR detailsText: This structure was determined with Reduced-Dimensionality NMR

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM MR19 U-15N,13C;20mM MES, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% azide; 90% H2O, 10% D2O90% H2O/10% D2O
21mM MR19 U-100%15N,5%13C;20mM MES, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% azide; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: na / pH: 6.5 / Pressure: ambient / Temperature: 298 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 INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1varian, inccollection
NMRPipe2.2F. Delaglio et. alprocessing
DYANA1.5P. Guentertstructure solution
DYANA1.5P. Guentertrefinement
RefinementMethod: distance geometry simulated annealing torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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