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- PDB-2k5k: Solution structure of RhR2 from Rhodobacter Sphaeroides. Northeas... -

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Basic information

Entry
Database: PDB / ID: 2k5k
TitleSolution structure of RhR2 from Rhodobacter Sphaeroides. Northeast Structural Genomics Consortium
Componentsuncharacterized protein RhR2
Keywordsstructural genomics / unknown function / RhR2 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologySuccinate dehydrogenase assembly factor 4 / Protein of unknown function (DUF1674) / DUF1674 domain-containing protein
Function and homology information
Biological speciesRhodobacter sphaeroides 2.4.1 (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsThe results from one bond HN-N NOEs, CSI analysis, residual dipolar couplings, and correlation time ...The results from one bond HN-N NOEs, CSI analysis, residual dipolar couplings, and correlation time measurement on the protein indicated that extensive parts of the C and N terminal regions of the RhR2 protein are highly disordered. The resonances for R26, R27, and R28 were not assigned due to signal overlap; therefore no restraints were used for this region. The ordered regions of the calculated RhR2 structure are residues 15 to 25 (four turn helix) and 28 to 31 (one turn helix).
AuthorsLee, H. / Bansal, S. / Chen, C.X. / Jiang, M. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. ...Lee, H. / Bansal, S. / Chen, C.X. / Jiang, M. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. / Montelione, G.T. / Prestegard, J.H. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution Structure of RhR2
Authors: Lee, H. / Bansal, S. / Montelione, G.T. / Prestegard, J.H.
History
DepositionJun 28, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3May 29, 2024Group: 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: uncharacterized protein RhR2


Theoretical massNumber of molelcules
Total (without water)8,2191
Polymers8,2191
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)10 / 50structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein uncharacterized protein RhR2


Mass: 8219.302 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides 2.4.1 (bacteria)
Species: sphaeroides / Strain: XL10 / Gene: RHOS4_27210, RSP_1104 / Plasmid: pET21 / Species (production host): coli / Production host: Escherichia coli (E. coli) / References: UniProt: Q3IYU5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D C(CO)NH
1413D HNCO
1513D HN(CA)CB
1613D H(CCO)NH
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1913D 1H-15N TOCSY
11013D 1H-13C NOESY
11122D 1H-15N HSQCTROSY

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Sample preparation

Details
Solution-IDContents
10.87 mM [U-100% 13C; U-100% 15N] RhR2, 0.2 % sodium azide, 100 mM DTT, 5 mM CaCl2, 100 mM sodium chloride, 20 mM MES, 95% H2O/5% D2O
20.74 mM [U-100% 13C; U-100% 15N] RhR2, 0.2 % sodium azide, 100 mM DTT, 5 mM CaCl2, 100 mM sodium chloride, 20 mM MES, 8 % Pentaethylene glycol monodecyl ether, 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.87 mMRhR2[U-100% 13C; U-100% 15N]1
0.2 %sodium azide1
100 mMDTT1
5 mMCaCl21
100 mMsodium chloride1
20 mMMES1
0.74 mMRhR2[U-100% 13C; U-100% 15N]2
0.2 %sodium azide2
100 mMDTT2
5 mMCaCl22
100 mMsodium chloride2
20 mMMES2
8 %Pentaethylene glycol monodecyl ether2
Sample conditionsIonic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
SparkyGoddardchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PSVSBhattacharya and Montelionedata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 10

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