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- PDB-2juw: NMR solution structure of homodimer protein SO_2176 from Shewanel... -

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Basic information

Entry
Database: PDB / ID: 2juw
TitleNMR solution structure of homodimer protein SO_2176 from Shewanella oneidensis. Northeast Structural Genomics Consortium target SoR77
ComponentsUPF0352 protein SO_2176
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / homodimer / helix / dimer / all alpha / Northeast Structural Genomics Consortium / NESG / PSI-2 / Protein Structure Initiative
Function / homologyUncharacterised protein family UPF0352 / YejL-like superfamily / Protein of unknown function (DUF1414) / YejL-like / YejL-like / Orthogonal Bundle / Mainly Alpha / UPF0352 protein SO_2176
Function and homology information
Biological speciesShewanella oneidensis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailshomodimer, all helix
AuthorsRamelot, T.A. / Cort, J.R. / Wang, D. / Nwosu, C. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. ...Ramelot, T.A. / Cort, J.R. / Wang, D. / Nwosu, C. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR solution structure of homodimer protein SO_2176 from Shewanella oneidensis. Northeast Structural Genomics Consortium target SoR77.
Authors: Ramelot, T.A. / Cort, J.R. / Montelione, G.T. / Kennedy, M.A.
History
DepositionSep 3, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPF0352 protein SO_2176
B: UPF0352 protein SO_2176


Theoretical massNumber of molelcules
Total (without water)17,8932
Polymers17,8932
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein UPF0352 protein SO_2176


Mass: 8946.255 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_2176 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMGK / References: UniProt: Q8EF26

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: homodimer, all helix
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D 1H-15N NOESY
1413D 1H-13C NOESY
1544D 1H-13C NOESY
1613D HNCO
1713D HN(CA)CB
1813D CBCA(CO)NH
1923D H(CCO)NH
11023D C(CO)NH
11123D HBHA(CO)NH
11213D (H)CCH-COSY
11332D 1H-13C HSQC
11442D 1H-15N HSQC
11522D 1H-15N HSQC
11632D 1H-15N HSQC
11723D CCH-TOCSY
11843D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] protein, 100 mM sodium chloride, 20 mM ammonium acetate, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
21 mM 50% NC labeled and 50% unlabeled protein mixed together to form mixed homodimer protein, 100 mM sodium chloride, 20 mM ammonium acetate, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
31 mM [U-5% 13C; U-100% 15N] protein, 100 mM sodium chloride, 20 mM ammonium acetate, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
41 mM [U-100% 13C; U-100% 15N] protein, 100 mM sodium chloride, 20 mM ammonium acetate, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein[U-100% 13C; U-100% 15N]1
100 mMsodium chloride1
20 mMammonium acetate1
5 mMcalcium chloride1
10 mMDTT1
0.02 %sodium azide1
1 mMprotein50% NC labeled and 50% unlabeled protein mixed together to form mixed homodimer2
100 mMsodium chloride2
20 mMammonium acetate2
5 mMcalcium chloride2
10 mMDTT2
0.02 %sodium azide2
1 mMprotein[U-5% 13C; U-100% 15N]3
100 mMsodium chloride3
20 mMammonium acetate3
5 mMcalcium chloride3
10 mMDTT3
0.02 %sodium azide3
1 mMprotein[U-100% 13C; U-100% 15N]4
100 mMsodium chloride4
20 mMammonium acetate4
5 mMcalcium chloride4
10 mMDTT4
0.02 %sodium azide4
Sample conditionsIonic strength: 0.1 / 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
NMRPipelinux9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMR6.1CVariancollection
AutoStructure2.1.1Huang, Tejero, Powers and Montelionedata analysis
X-PLOR NIH2.15.0Schwieters, Kuszewski, Tjandra and Clorestructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky3.1Goddarddata analysis
PSVS1.3Bhattacharya and Montelionestructure validation
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Xplor-NIH
NMR constraintsNOE constraints total: 1362 / NOE intraresidue total count: 0 / NOE long range total count: 424 / NOE medium range total count: 734 / NOE sequential total count: 204 / Hydrogen bond constraints total count: 2 / Protein chi angle constraints total count: 0 / Protein phi angle constraints total count: 63 / Protein psi angle constraints total count: 63
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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