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- PDB-2k6v: Solution structures of apo Sco1 protein from Thermus Thermophilus -

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Basic information

Entry
Database: PDB / ID: 2k6v
TitleSolution structures of apo Sco1 protein from Thermus Thermophilus
ComponentsPutative cytochrome c oxidase assembly protein
KeywordsELECTRON TRANSPORT / Thioredoxin fold / Electron transfer protein / metal binding protein
Function / homology
Function and homology information


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
Cytochrome c oxidase assembly protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model type detailsminimized average
AuthorsAbriata, L.A. / Banci, L. / Bertini, I. / Ciofi-Baffoni, S. / Gkazonis, P. / Spyroulias, G.A. / Vila, A.J. / Wang, S.
CitationJournal: Nat.Chem.Biol. / Year: 2008
Title: Mechanism of Cu(A) assembly.
Authors: Abriata, L.A. / Banci, L. / Bertini, I. / Ciofi-Baffoni, S. / Gkazonis, P. / Spyroulias, G.A. / Vila, A.J. / Wang, S.
History
DepositionJul 28, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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 1.3May 22, 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: Putative cytochrome c oxidase assembly protein


Theoretical massNumber of molelcules
Total (without water)19,1691
Polymers19,1691
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)31 / 31structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Putative cytochrome c oxidase assembly protein


Mass: 19168.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1942 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SGY8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1323D CBCA(CO)NH
1423D HNCO
1523D HNCA
1623D HN(CA)CB
1723D (H)CCH-TOCSY
1823D HBHA(CO)NH
1913D 1H-15N NOESY
11023D 1H-13C NOESY
111115N R2
112115N R1
11311H-15N NOE

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMentity[U-100% 15N]1
0.8 mMentity[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 50mM Pi / pH: 7.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE5002
Bruker AvanceBrukerAVANCE6003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CARAKeller, R. et al.chemical shift assignment
CARAKeller, R. et al.peak picking
CARAKeller, R. et al.data analysis
CYANAGuntert, P. et al.structure solution
AmberCase, D. et al.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2162 / NOE intraresidue total count: 637 / NOE long range total count: 565 / NOE medium range total count: 352 / NOE sequential total count: 608 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 84 / Protein psi angle constraints total count: 93
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 31 / Conformers submitted total number: 31

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