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- PDB-2jz2: Solution NMR structure of Ssl0352 protein from Synechocystis sp. ... -

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Basic information

Entry
Database: PDB / ID: 2jz2
TitleSolution NMR structure of Ssl0352 protein from Synechocystis sp. PCC 6803. Northeast Structural Genomics Consortium target SgR42
ComponentsSsl0352 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / SH3-like / Synechocystis sp. PCC 6803 / Ssl0352 protein / target SgR42 / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyNADH dehydrogenase-like complex, subunit S / NAD(P)H dehydrogenase subunit S / photosynthetic electron transport chain / SH3 type barrels. - #140 / SH3 type barrels. / Roll / Mainly Beta / Ssl0352 protein
Function and homology information
Biological speciesSynechocystis sp. (bacteria)
MethodSOLUTION NMR / simulated annealing, simulated annealing in explicit water bath
AuthorsEletsky, A. / Sukumaran, D. / Wang, D. / Hamilton, K. / Foote, E.L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. ...Eletsky, A. / Sukumaran, D. / Wang, D. / Hamilton, K. / Foote, E.L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of Ssl0352 protein from Synechocystis sp.
Authors: Eletsky, A. / Sukumaran, D. / Wang, D. / Hamilton, K. / Foote, E.L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Rost, B. / Acton, T.B. / Montelione, G.T. / Szyperski, T.
History
DepositionDec 22, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ssl0352 protein


Theoretical massNumber of molelcules
Total (without water)7,6561
Polymers7,6561
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Ssl0352 protein


Mass: 7655.642 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: ssl0352 / Plasmid: pET21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: P74795

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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 aliphatic
1312D 1H-13C HSQC aromatic
1412D 1H-13C CT-HSQC aliphatic
1512D 1H-13C CT-HSQC aromatic
1613D HNCO
171(4,3)D GFT CABCA(CO)NHN
181(4,3)D GFT HNNCABCA
191(4,3)D GFT HABCAB(CO)NHN
1101(4,3)D GFT (H)CCH-COSY aliphatic
11113D (H)CCH-TOCSY aliphatic
1121(4,3)D GFT (H)CCH-COSY aromatic
11313D 1H-15N,13C NOESY
11422D 1H-13C CT-HSQC 28ms methyl
11522D 1H-13C CT-HSQC 56ms methyl

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Sample preparation

Details
Solution-IDContentsSolvent system
11.17 mM [U-100% 13C; U-100% 15N] SgR42 protein, 5 mM calcium chloride, 100 mM sodium chloride, 20 mM ammonium acetate, 10 mM DTT, 0.03 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
21.17 mM [U-5% 13C; U-100% 15N] SgR42 protein, 5 mM calcium chloride, 100 mM sodium chloride, 20 mM ammonium acetate, 10 mM DTT, 0.03 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.17 mMSgR42 protein[U-100% 13C; U-100% 15N]1
5 mMcalcium chloride1
100 mMsodium chloride1
20 mMammonium acetate1
10 mMDTT1
0.03 %sodium azide1
1.17 mMSgR42 protein[U-5% 13C; U-100% 15N]2
5 mMcalcium chloride2
100 mMsodium chloride2
20 mMammonium acetate2
10 mMDTT2
0.03 %sodium azide2
Sample conditionsIonic strength: 135 / pH: 5.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJ2.1BVariancollection
PROSA6.0.2Guntertprocessing
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichpeak picking
CSI2Wishart and Sykesdata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.1.1Huang, Tejero, Powers and Montelionestructure solution
AutoAssign1.15.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.data analysis
RefinementMethod: simulated annealing, simulated annealing in explicit water bath
Software ordinal: 1 / Details: CYANA, CNS
NMR constraintsNOE constraints total: 578 / NOE intraresidue total count: 147 / NOE long range total count: 226 / NOE medium range total count: 57 / NOE sequential total count: 148
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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