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- PDB-2gzo: NMR structure of UPF0301 PROTEIN SO3346 from Shewanella oneidensi... -

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Basic information

Entry
Database: PDB / ID: 2gzo
TitleNMR structure of UPF0301 PROTEIN SO3346 from Shewanella oneidensis: Northeast Structural Genomics Consortium target SOR39
ComponentsUPF0301 protein SO3346
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / GFT-NMR / PROTEIN STRUCTURE / NESGC / ALPHA-BETA / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


VC0467-like domains / VC0467-like / VC0467-like / Protein of unknown function UPF0301 / Uncharacterized ACR, COG1678 / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
UPF0301 protein SO_3346
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsSingarapu, K.K. / Liu, G. / Eletsky, A. / Xu, D. / Sukumaran, D.K. / Mei, J. / Xiao, R. / Cunningham, K. / Ma, L.C. / Ritu, S. ...Singarapu, K.K. / Liu, G. / Eletsky, A. / Xu, D. / Sukumaran, D.K. / Mei, J. / Xiao, R. / Cunningham, K. / Ma, L.C. / Ritu, S. / Acton, T.B. / Rost, B. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR structure of UPF0301 PROTEIN SO3346 from Shewanella oneidensis: Northeast Structural Genomics Consortium target SOR39
Authors: Singarapu, K.K. / Liu, G. / Eletsky, A. / Xu, D. / Sukumaran, D.K. / Mei, J. / Xiao, R. / Cunningham, K. / Ma, L.C. / Ritu, S. / Acton, T.B. / Rost, B. / Montelione, G.T. / Szyperski, T.
History
DepositionMay 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0301 protein SO3346


Theoretical massNumber of molelcules
Total (without water)21,7951
Polymers21,7951
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 least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein UPF0301 protein SO3346


Mass: 21795.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: XL-10 / Gene: SO3346 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q8EBZ9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111[4,3]D GFT, HNNCABCA
121[4,3]D GFT, CABCA(CO)NHN
131[4,3]D GFT ALI-(H)CCH
141[4,3]D GFT ARO-(H)CCH
151[4,3]D GFT, HABCAB(CO)NHN
161SIMULTANIOUS HETERONUCLEAR RESOLVED [1H, 1H]-NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: MC2023, 50mM Arginine, 10mM DTT, 50mM Bis Tris pH 6.5, 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.5Frank Delaglio, et alprocessing
DYANA1.5Peter Guntert., et aldata analysis
AutoStructure2.0.0Huang, Y. J., et aldata analysis
CYANA2.1Peter Guntert., et alrefinement
CNS1.1A.T.Brunger., et alrefinement
XEASY1.3.11Bartels, C., et aldata analysis
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
Details: The structures are based on a total of restraints, 1828 are NOE-derived distance constraints, 126 dihedral angle restraints, 35 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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