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- PDB-2gvp: Solution structure of Human apo Sco1 -

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Basic information

Entry
Database: PDB / ID: 2gvp
TitleSolution structure of Human apo Sco1
ComponentsSCO1 protein homolog, mitochondrial
KeywordsTRANSPORT PROTEIN / Thioredoxin-like fold / metalloprotein / Structural Genomics / Structural Proteomics in Europe / SPINE
Function / homology
Function and homology information


Complex IV assembly / copper chaperone activity / mitochondrial cytochrome c oxidase assembly / myofibril / intracellular copper ion homeostasis / mitochondrial inner membrane / copper ion binding / mitochondrion
Similarity search - Function
Synthesis of cytochrome c oxidase, Sco1/Sco2 / Copper chaperone SCO1/SenC / SCO1/SenC / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein SCO1 homolog, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model type detailsminimized average
AuthorsBanci, L. / Bertini, I. / Calderone, V. / Ciofi-Baffoni, S. / Mangani, S. / Paulmaa, P. / Martinelli, M. / Wang, S. / Structural Proteomics in Europe (SPINE)
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: A hint for the function of human Sco1 from different structures.
Authors: Banci, L. / Bertini, I. / Calderone, V. / Ciofi-Baffoni, S. / Mangani, S. / Martinelli, M. / Palumaa, P. / Wang, S.
History
DepositionMay 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 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_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 protein homolog, mitochondrial


Theoretical massNumber of molelcules
Total (without water)19,7121
Polymers19,7121
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)1 / -
RepresentativeModel #1minimized average structure

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Components

#1: Protein SCO1 protein homolog, mitochondrial


Mass: 19712.277 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN (residues 132-301)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCO1, SCOD1 / Plasmid: pETG-30A / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21DE3 GOLD / References: UniProt: O75880

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY
131CBCA(CO)NH
141HNCA
151HN(CO)CA
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM Human Sco1 U-15N,13C, 50mM phosphate buffer NA, 90% H2O, 10% D2O90% H2O/10% D2O
21mM Human Sco1 U-15N, 50mM phosphate buffer NA, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 50mM sodium phosphate / pH: 7.2 / 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
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE9002
Bruker AVANCEBrukerAVANCE5003

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Processing

NMR software
NameVersionClassification
XwinNMR3.5collection
XwinNMR3.5processing
CARA2.1data analysis
DYANA1.5structure solution
Amber8refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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