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- PDB-2jr5: Solution structure of UPF0350 protein VC_2471. Northeast Structur... -

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Basic information

Entry
Database: PDB / ID: 2jr5
TitleSolution structure of UPF0350 protein VC_2471. Northeast Structural Genomics Target VcR36
ComponentsUPF0350 protein VC_2471
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / UPF0350 protein VC_2471 / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


succinate metabolic process / cytoplasm
Similarity search - Function
Flavinator of succinate dehydrogenase / Flavinator of succinate dehydrogenase / Flavinator of succinate dehydrogenase superfamily / Flavinator of succinate dehydrogenase / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FAD assembly factor SdhE
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsWu, Y. / Parish, D. / Singarapu, K.K. / Sukumaran, D. / Eletski, A. / Shastry, R. / Nwosu, C. / Maglaqui, M. / Xiao, R. / Liu, J. ...Wu, Y. / Parish, D. / Singarapu, K.K. / Sukumaran, D. / Eletski, A. / Shastry, R. / Nwosu, C. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
Citation
#1: Journal: Biochemistry / Year: 2012
Title: Solution NMR structure of yeast succinate dehydrogenase flavinylation factor sdh5 reveals a putative sdh1 binding site.
Authors: Eletsky, A. / Jeong, M.Y. / Kim, H. / Lee, H.W. / Xiao, R. / Pagliarini, D.J. / Prestegard, J.H. / Winge, D.R. / Montelione, G.T. / Szyperski, T.
History
DepositionJun 20, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2013Group: Database references
Revision 1.4Feb 19, 2020Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _struct_ref_seq_dif.details
Revision 1.5Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.6May 8, 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

Downloads & links

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Assembly

Deposited unit
A: UPF0350 protein VC_2471


Theoretical massNumber of molelcules
Total (without water)10,9361
Polymers10,9361
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 UPF0350 protein VC_2471


Mass: 10936.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: El Tor Inaba N16961 / Gene: VC_2471 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q9KPA2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1114,3D, GFT HNNCABCA
1214,3D, GFT CABCACONNH
1314,3D, GFT (H)CCH COSY
1413D, 15N-13C RESOLVEDSIMULTANEOUS NOESY
1513D HNCO
1612D 1H-15N HSQC
1722D 1H-13C HSQC
1813D CBCA(CO)NH
1913D HN(CA)CB

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM [U-100% 13C; U-100% 15N] entity, 90% H2O/10% D2O90% H2O/10% D2O
21.1 mM [U-5% 13C; U-100% 15N] entity, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMentity[U-100% 13C; U-100% 15N]1
1.1 mMentity[U-5% 13C; U-100% 15N]2
Sample conditionsIonic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 25 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
AutoStructureHuang, Tejero, Powers and Montelionestructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
XEASYBartels et al.peak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
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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