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- PDB-2kzv: Solution NMR structure of CV_0373(175-257) protein from Chromobac... -

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Basic information

Entry
Database: PDB / ID: 2kzv
TitleSolution NMR structure of CV_0373(175-257) protein from Chromobacterium violaceum, Northeast Structural Genomics Consortium Target CvR118A
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown function / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


RNA nuclease activity
Similarity search - Function
NYN domain, MARF1-type / NYN domain / LOTUS domain-like / OST-HTH/LOTUS domain / LOTUS-like domain / OST-HTH/LOTUS domain / OST-type HTH domain profile. / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
HTH OST-type domain-containing protein
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsYang, Y. / Ramelot, T.A. / Wang, D. / Ciccosanti, C. / Mao, L. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. ...Yang, Y. / Ramelot, T.A. / Wang, D. / Ciccosanti, C. / Mao, L. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of CV_0373(175-257) protein from Chromobacterium violaceum, Northeast Structural Genomics Consortium Target CvR118A.
Authors: Yang, Y. / Ramelot, T.A. / Wang, D. / Ciccosanti, C. / Mao, L. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A.
History
DepositionJun 25, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 1.3Jun 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 15, 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:
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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)10,6031
Polymers10,6031
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 / 150structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein


Mass: 10602.881 Da / Num. of mol.: 1 / Fragment: sequence database residues 175-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Gene: CV_0373 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pMGK / References: UniProt: Q7P141

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC CT
1313D 1H-15N NOESY
1413D 1H-13C NOESY
1513D HNCO
1613D HNCA
1713D HN(CA)CB
1813D CBCA(CO)NH
1913D HN(CO)CA
11013D HBHA(CO)NH
11113D H(CCO)NH
11213D C(CO)NH
11313D (H)CCH-TOCSY
11413D (H)CCH-COSY
11533D (H)CCH-TOCSY
11634D CC NOESY
11712D 1H-15N HSQC swN150ppm

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9 mM [U-100% 13C; U-100% 15N] CV_0373(175-257) protein from Chromobacterium violaceum, 20 mM ammonium acetate, 100 mM sodium chloride 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.82 mM [U-5% 13C; U-100% 15N] CV_0373(175-257) protein from Chromobacterium violaceum, 20 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
30.9 mM [U-100% 13C; U-100% 15N] CV_0373(175-257) protein from Chromobacterium violaceum, 20 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMCV_0373(175-257) protein from Chromobacterium violaceum-1[U-100% 13C; U-100% 15N]1
20 mMammonium acetate-21
100 mMsodium chloride-31
5 mMcalcium chloride-41
10 mMDTT-51
0.02 %sodium azide-61
0.82 mMCV_0373(175-257) protein from Chromobacterium violaceum-7[U-5% 13C; U-100% 15N]2
20 mMammonium acetate-82
100 mMsodium chloride-92
5 mMcalcium chloride-102
10 mMDTT-112
0.02 %sodium azide-122
0.9 mMCV_0373(175-257) protein from Chromobacterium violaceum-13[U-100% 13C; U-100% 15N]3
20 mMammonium acetate-143
100 mMsodium chloride-153
5 mMcalcium chloride-163
10 mMDTT-173
0.02 %sodium azide-183
Sample conditionsIonic strength: 0.2 / pH: 4.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceIIIBrukerAVANCE III8502

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2008Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMR6.1CVariancollection
TopSpin2.1.4Bruker 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 Montelionerefinement
AutoAssign2.3Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
PdbStat5.1(PdbStat)-Roberto Tejero and Gaetano T. Montelionestructure solution
PINE Server1Bahrami, A., Assadi, A., Markley, J. L. & Eghbalnia, H.autoassignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Xplor-nih with HBDB
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 20

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