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- PDB-1on4: Solution structure of soluble domain of Sco1 from Bacillus Subtilis -

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Basic information

Entry
Database: PDB / ID: 1on4
TitleSolution structure of soluble domain of Sco1 from Bacillus Subtilis
ComponentsSco1
KeywordsMETAL BINDING PROTEIN / COX assembly protein / copper protein / Sco1 from B. subtilis / thioredoxin-like fold / YPMQ / Structural Proteomics in Europe / SPINE / Structural Genomics
Function / homology
Function and homology information


metal ion binding / plasma membrane
Similarity search - Function
Copper chaperone SCO1/SenC / SCO1/SenC / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SCO1 protein homolog
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics coupled to simulated annealing, restrained energy minimization
AuthorsBalatri, E. / Banci, L. / Bertini, I. / Cantini, F. / Ciofi-Baffoni, S. / Structural Proteomics in Europe (SPINE)
CitationJournal: STRUCTURE / Year: 2003
Title: Solution Structure of Sco1: A Thioredoxin-like Protein Involved in Cytochrome c Oxidase Assembly
Authors: Balatri, E. / Banci, L. / Bertini, I. / Cantini, F. / Ciofi-Baffoni, S.
History
DepositionFeb 27, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 / 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 / _pdbx_nmr_spectrometer.model / _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: Sco1


Theoretical massNumber of molelcules
Total (without water)19,8561
Polymers19,8561
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)30 / 300target function
Representative

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Components

#1: Protein Sco1 / Hypothetical protein ypmQ


Mass: 19856.350 Da / Num. of mol.: 1 / Fragment: soluble domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: YPMQ / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)pLysS / References: UniProt: P54178

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111CBCANH
121CBCA(CO)NH
131HNCO
141HN(CA)CO
151(H)CCH-TOCSY
1642D NOESY
1723D 15N-separated NOESY
1813D 13C-separated NOESY
192HNHA
11032D NOESY
NMR detailsText: HNHB experiments and TOCSY 2D were also acquired

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Sample preparation

Details
Solution-IDContentsSolvent system
113C and 15N labeled sample100mM potassium phosphate buffer and 2mM DTT, pH 7, containing 10% D2O
215N labeled sample100mM potassium phosphate buffer and 2mM DTT, pH 7, containing 10% D2O
3unlabeled sample100mM potassium phosphate buffer and 2mM DTT, pH 7, containing 10% D2O
4unlabeled sample100mM potassium phosphate buffer and 2mM DTT, pH 7, contaning 90% D2O
Sample conditionsIonic strength: 100mM potassium phosphate / pH: 7 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE7003
Bruker AVANCEBrukerAVANCE8004

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Processing

NMR software
NameVersionClassification
XwinNMRcollection
XEASYversion 1.3data analysis
GARANT2data analysis
DYANA1.5structure solution
CYANA1structure solution
Amber5refinement
XwinNMRprocessing
RefinementMethod: torsion angle dynamics coupled to simulated annealing, restrained energy minimization
Software ordinal: 1
Details: the structures are based on a total of 3492 NOE-derived distance constraints, 181 dihedral angle restraints and 88 stereospecifically assigned proton pairs
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 300 / Conformers submitted total number: 30

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