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- PDB-2kon: NMR solution structure of CV_2116 from Chromobacterium violaceum.... -

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Basic information

Entry
Database: PDB / ID: 2kon
TitleNMR solution structure of CV_2116 from Chromobacterium violaceum. Northeast Structural Genomics Consortium Target CvT4(1-82)
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / uncharacterized protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyDouble Stranded RNA Binding Domain - #350 / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesChromobacterium violaceum (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsYang, Y. / Ramelot, T.A. / Cort, J.R. / Garcia, M. / Yee, A. / Arrowsmith, C.H. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR solution structure of CV_2116 from Chromobacterium violaceum.Northeast Structural Genomics Consortium Target CvT4(1-82)
Authors: Yang, Y. / Ramelot, T.A. / Cort, J.R. / Garcia, M. / Yee, A. / Arrowsmith, C.H. / Montelione, G.T. / Kennedy, M.A.
History
DepositionSep 24, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Jun 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 1.4May 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

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)9,4441
Polymers9,4441
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 150structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein


Mass: 9443.607 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Gene: CV_2116 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q7NW74

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: NMR solution structure of CV_2116 from Chromobacterium violaceum
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1322D 1H-13C HSQC
1413D 1H-15N NOESY
1513D 1H-13C NOESY
1613D HNCO
1713D HNCA
1813D HN(CA)CB
1913D CBCA(CO)NH
11013D HN(CO)CA
11113D HBHA(CO)NH
11213D C(CO)NH
11313D (H)CCH-TOCSY
11413D (H)CCH-COSY
11533D (H)CCH-TOCSY
11634D CC NOESY
11712D His-HMQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-100% 13C; U-100% 15N] CV_2116, 10 mM TRIS, 300 mM sodium chloride, 10 uM zinc sulfate, 10 mM DTT, 1 mM benzamidine, 1x v/v inhibitor cocktail, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM CV_2116, 10 mM TRIS, 300 mM sodium chloride, 10 uM zinc sulfate, 10 mM DTT, 1 mM benzamidine, 1x v/v inhibitor cocktail, 90% H2O/10% D2O90% H2O/10% D2O
30.8 mM [U-100% 13C; U-100% 15N] CV_2116, 10 mM TRIS, 300 mM sodium chloride, 10 uM zinc sulfate, 10 mM DTT, 1 mM benzamidine, 1x v/v inhibitor cocktail, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMCV_2116-1[U-100% 13C; U-100% 15N]1
10 mMTRIS-21
300 mMsodium chloride-31
10 uMzinc sulfate-41
10 mMDTT-51
1 mMbenzamidine-61
1 v/vinhibitor cocktail-71
0.8 mMCV_2116-82
10 mMTRIS-92
300 mMsodium chloride-102
10 uMzinc sulfate-112
10 mMDTT-122
1 mMbenzamidine-132
1 v/vinhibitor cocktail-142
0.8 mMCV_2116-15[U-100% 13C; U-100% 15N]3
10 mMTRIS-163
300 mMsodium chloride-173
10 uMzinc sulfate-183
10 mMDTT-193
1 mMbenzamidine-203
1 v/vinhibitor cocktail-213
Sample conditionsIonic strength: 0.2 / pH: 7.0 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA7503

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2008Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMR6.1CVariancollection
TopSpin2.1.3Bruker Biospincollection
AutoStructure2.2.1Huang, Tejero, Powers and Montelionedata analysis
X-PLOR NIH2.2Schwieters, Kuszewski, Tjandra and Clorestructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky3.113Goddarddata analysis
PSVS1.4Bhattacharya and Montelionestructure solution
AutoAssign2.3Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
PdbStat5.1(PdbStat)-Roberto Tejero and Gaetano T. Montelionestructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Xplor-nih-2.20 with HBDB
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 150 / Conformers submitted total number: 20

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