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- PDB-1u3n: A SOD-like protein from B. subtilis, unstructured in solution, be... -

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Basic information

Entry
Database: PDB / ID: 1u3n
TitleA SOD-like protein from B. subtilis, unstructured in solution, becomes ordered in the crystal: implications for function and for fibrillogenesis
ComponentsHypothetical superoxide dismutase-like protein yojM
KeywordsUNKNOWN FUNCTION / SOD-like / Bacillus subtilis / BsSOD / solution structure / NMR / Metalloprotein
Function / homology
Function and homology information


ion binding / superoxide dismutase activity / removal of superoxide radicals / copper ion binding / zinc ion binding / identical protein binding / plasma membrane
Similarity search - Function
Prokaryotic lipoprotein-attachment site / Prokaryotic lipoprotein-attachment site / Superoxide dismutase, copper/zinc binding domain / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Superoxide dismutase-like protein YojM
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / the structure of SOD-like from bacillus subtilis was determined using triple resonance three-, bi-dimensional, homonuclear bi-dimensional NMR technique
AuthorsBanci, L. / Bertini, I. / Calderone, V. / Cramaro, F. / Del Conte, R. / Fantoni, A. / Mangani, S. / Quattrone, A. / Viezzoli, M.S.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: A prokaryotic superoxide dismutase paralog lacking two Cu ligands: from largely unstructured in solution to ordered in the crystal.
Authors: Banci, L. / Bertini, I. / Calderone, V. / Cramaro, F. / Del Conte, R. / Fantoni, A. / Mangani, S. / Quattrone, A. / Viezzoli, M.S.
History
DepositionJul 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical superoxide dismutase-like protein yojM


Theoretical massNumber of molelcules
Total (without water)17,2511
Polymers17,2511
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / -target function
Representative

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Components

#1: Protein Hypothetical superoxide dismutase-like protein yojM


Mass: 17251.041 Da / Num. of mol.: 1 / Fragment: SOD-like
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: YOJM, BSU19400 / Plasmid: pPMSOD159 / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP1 / References: UniProt: O31851

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
112CBCANH, CBCA(CO)NH, HNCO, HN(CA)CO, CCC(CO)NH, 13C-HSQC, H(C)CH-TOCSY, (H)CCH-TOCSY, 13C-NOESY-HSQC
12115N-HSQC, 15N-CLEANEX, HNHA, HNHB, 15N-HSQC-NOESY, NOESY
NMR detailsText: the structure of SOD-like from bacillus subtilis was determined using triple resonance three- and bi-dimensional and homonuclear bi-dimensional NMR technique

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Sample preparation

Details
Solution-IDContentsSolvent system
115N labelled BsSOD about 1.5mMH2O with 10% D2O
215N, 13C labelled BsSOD about 1.5mMH2O wiht 10% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
17.4 1 atm298 K
27.4 1 atm284 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE8003
Bruker AVANCEBrukerAVANCE7004

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Processing

NMR software
NameClassification
CALIBAdata analysis
DYANArefinement
XwinNMRcollection
PROCHECKdata analysis
RefinementMethod: the structure of SOD-like from bacillus subtilis was determined using triple resonance three-, bi-dimensional, homonuclear bi-dimensional NMR technique
Software ordinal: 1
NMR ensembleConformer selection criteria: target function / Conformers submitted total number: 30

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