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- PDB-2n47: EC-NMR Structure of Synechocystis sp. PCC 6803 Slr1183 Determined... -

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Basic information

Entry
Database: PDB / ID: 2n47
TitleEC-NMR Structure of Synechocystis sp. PCC 6803 Slr1183 Determined by Combining Evolutionary Couplings (EC) and Sparse NMR Data. Northeast Structural Genomics Consortium target SgR145
ComponentsSlr1183 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / EC-NMR / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / Protein Structure Initiative / PSI-Biology
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 sp. PCC 6803 substr. Kazusa (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsTang, Y. / Huang, Y.J. / Hopf, T.A. / Sander, C. / Marks, 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
DepositionJun 17, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Database references
Revision 1.2Aug 12, 2015Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Remark 0THIS ENTRY 2N47 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA IN 2KW5 DETERMINED ...THIS ENTRY 2N47 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA IN 2KW5 DETERMINED BY AUTHORS: P.ROSSI,F.FOROUHAR,H.LEE,O.LANGE,B.MAO,A.LEMAK,M.MAGLAQUI,R.BELOTE,C.CICCOSANTI,E.FOOTE,S.SAHDEV,T.ACTON,R.XIAO,J.EVERETT,D.BAKER,G.T.MONTELIONE,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG)

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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 / 100lowest 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 sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa / Gene: slr1183 / Production host: Escherichia coli (E. coli) / References: UniProt: P74712

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: AUTHOR USED THE EXPERIMENTAL DATA FROM ENTRY 2KW5.

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Processing

NMR software
NameDeveloperClassification
RosettaD. Bakerrefinement
EVfold-plmdata analysis
ASDPdata analysis
CYANAGuntert, P., Mumenthaler, C. and Wuthrich, K.data analysis
EC-NMRdata analysis
TALOS+data analysis
ReduceJ. Richardson and D. Richardsonrefinement
CYANAGuntert, P., Mumenthaler, C. and Wuthrich, K.structure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: Protons from the Rosetta models were removed and added back using Reduce.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: lowest energy / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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