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- PDB-2kw5: Solution NMR Structure of the Slr1183 protein from Synechocystis ... -

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Basic information

Entry
Database: PDB / ID: 2kw5
TitleSolution NMR Structure of the Slr1183 protein from Synechocystis sp. PCC 6803, Northeast Structural Genomics Consortium Target SgR145
ComponentsSlr1183 protein
KeywordsStructural Genomics / Unknown function / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-2 / Protein Structure Initiative
Function / homologyMethyltransferase domain 25 / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Slr1183 protein
Function and homology information
Biological speciesSynechocystis (bacteria)
MethodSOLUTION NMR
Model detailslowest energy, model 1
AuthorsRossi, P. / Forouhar, F. / Lee, H. / Lange, O. / Mao, B. / Lemak, A. / Maglaqui, M. / Belote, R. / Ciccosanti, C. / Foote, E. ...Rossi, P. / Forouhar, F. / Lee, H. / Lange, O. / Mao, B. / Lemak, A. / Maglaqui, M. / Belote, R. / Ciccosanti, C. / Foote, E. / Sahdev, S. / Acton, T. / Xiao, R. / Everett, J. / Baker, D. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples.
Authors: Lange, O.F. / Rossi, P. / Sgourakis, N.G. / Song, Y. / Lee, H.W. / Aramini, J.M. / Ertekin, A. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Baker, D.
History
DepositionMar 31, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 27, 2012Group: Database references
Revision 1.3Jul 18, 2012Group: Database references
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Slr1183 protein


Theoretical massNumber of molelcules
Total (without water)22,4031
Polymers22,4031
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Slr1183 protein


Mass: 22403.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis (bacteria) / Strain: PCC 6803 / Gene: slr1183 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P74712

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1612D 1H-15N HSQC
1712D 1H-15N HSQC
1813D HNCA(CO)
1913D HNCA
11013D 1H-13C NOESY
11113D 1H-15N NOESY
11213D 1H-13C HSQC NOESY HSQC
11313D 1H-15N HSQC NOESY HSQC
11413D 1H-13C-15N HSQC NOESY HSQC
11513D 1H-15N-13C HSQC NOESY HSQC
11613D (H)CCH-TOCSY
11711D 15N T1
11811D 15N T2 CPMG
11912D- HET NOE

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Sample preparation

DetailsContents: 1.1 mM [U-100% 13C; U-100% 15N] SgR145, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
SampleConc.: 1.1 mM / Component: SgR145-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
VnmrJVariancollection
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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