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- PDB-2k0m: Solution NMR structure of the uncharacterized protein from Rhodos... -

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Basic information

Entry
Database: PDB / ID: 2k0m
TitleSolution NMR structure of the uncharacterized protein from Rhodospirillum rubrum gene locus Rru_A0810. Northeast Structural Genomics Target RrR43
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyProtein of unknown function (DUF3223) / Nuclear Transport Factor 2; Chain: A, - #40 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesRhodospirillum rubrum ATCC 11170 (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsRossi, P. / Wang, H. / Jiang, M. / Foote, E.L. / Xiao, R. / Liu, J. / Swapna, G. / Acton, T.B. / Baran, M.C. / Rost, B. ...Rossi, P. / Wang, H. / Jiang, M. / Foote, E.L. / Xiao, R. / Liu, J. / Swapna, G. / Acton, T.B. / Baran, M.C. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of the uncharacterized protein from Rhodospirillum rubrum gene locus Rru_A0810. Northeast Structural Genomics Target RrR43.
Authors: Rossi, P. / Xiao, R. / Acton, T.B. / Montelione, G.T.
History
DepositionFeb 4, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)11,8711
Polymers11,8711
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein


Mass: 11870.565 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum ATCC 11170 (bacteria)
Species: Rhodospirillum rubrum / Strain: NCIB 8255 / Gene: Rru_A0810 / Plasmid: pET21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q2RW81

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1222D 1H-13C HSQC
1323D HNCO
1423D HNCA
1523D HN(CA)CB
1623D HBHA(CO)NH
1723D (H)CCH-COSY
1823D (H)CCH-TOCSY
1923D CCH-TOCSY
11023D CBCA(CO)NH
11123D 1H-15N NOESY
11223D 1H-13C NOESY
11312D 1H-13C HSQC
NMR detailsText: MONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING. STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS BY CYANA2.1. 20 OF 100 STRUCTURES LOWEST TARGET FUNCTION ...Text: MONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING. STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS BY CYANA2.1. 20 OF 100 STRUCTURES LOWEST TARGET FUNCTION SELECTED. MODELS ARE FURTHER REFINED USING CNS IN EXPLICIT WATER SHELL (NILGES PROTOCOL WITH PARAM19). ASSIGNMENT STATS (EXCLUDING C-TERM TAG): BACKBONE 94.7%, SIDECHAIN 93.1%, AROMATIC (SC) 100%, VL METHYL STEREOSPECIFIC 100%, UNAMBIGUOUS SIDECHAIN NH2 100%. STRUCTURE BASED ON 1727 NOE. MAX NOE VIOLATION 0.25 A (1MODEL). 6 TOTAL CLOSE CONTACTS PER 20 MODELS. STRUCTURE QUALITY FACTOR (PSVS 1.3): ORDERED RESIDUES RANGES - 6-70, 75-94 (FOR [S(PHI)+S(PSI)] > 1.8) RMSD 0.6 BB, 1.0 ALL HEAVY ATOMS. SECONDARY STRUCTURE ELEMENTS ALPHA HELICES: (17-30, 39-50, 55-59), BETA STRANDS: (7-9, 12-14, 35-36, 63-70, 76-82, 87-89). RAMA. DISTRIBUTION: 90.2/9.7/0.1/0.1. PROCHECK (PSI-PHI): -0.29/-0.83 (RAW/Z), PROCHECK (ALL): -0.22/-1.30 (RAW/Z), MOLPROBITY CLASH: 15.46/-1.13 (RAW/Z). RPF SCORES ALL ASSIGNED RESIDUES (FIT OF NOESY PEAKLISTS TO STRUCTURE): RECALL: 0.917, PRECISION: 0.895, F-MEASURE: 0.906, DP-SCORE: 0.738.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.15 mM [U-5% 13C; U-100% 15N] RrR43, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 100 mM sodium chloride, 50 uM DSS, 5 mM calcium chloride, 90% H2O/10% D2O90% H2O/10% D2O
21.05 mM [U-100% 13C; U-100% 15N] RrR43, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 100 mM sodium chloride, 50 uM DSS, 5 mM calcium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.15 mMRrR43[U-5% 13C; U-100% 15N]1
20 mMMES1
10 mMDTT1
0.02 %sodium azide1
100 mMsodium chloride1
50 uMDSS1
5 mMcalcium chloride1
1.05 mMRrR43[U-100% 13C; U-100% 15N]2
20 mMMES2
10 mMDTT2
0.02 %sodium azide2
100 mMsodium chloride2
50 uMDSS2
5 mMcalcium chloride2
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
AutoAssign2.4.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PSVSBhattacharya and Montelionevalidation
TALOSCornilescu, Delaglio and Baxgeometry optimization
TopSpin1.3Bruker Biospincollection
Sparky3.112Goddarddata analysis
MOLMOL2k2Koradi, Billeter and Wuthrichvisualization
ProcheckNMRLaskowski and MacArthurrefinement
MolProbityRichardsonvalidation
RefinementMethod: molecular dynamics / 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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