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- PDB-1sp0: Solution Structure of apoCox11 -

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Basic information

Entry
Database: PDB / ID: 1sp0
TitleSolution Structure of apoCox11
ComponentsCytochrome C oxidase assembly protein ctaG
KeywordsMETAL TRANSPORT / immunoglobulin-like fold / copper protein / cytochrome c oxidase assembly
Function / homology
Function and homology information


respiratory chain complex IV assembly / copper ion binding / plasma membrane
Similarity search - Function
Ctag/Cox11 (Pfam 04442) / Ctag/Cox11 / Cytochrome c oxidase assembly protein CtaG/Cox11 / Cytochrome c oxidase assembly protein CtaG/Cox11, domain superfamily / Cytochrome c oxidase assembly protein CtaG/Cox11 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cytochrome c oxidase assembly protein CtaG
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing, restrained energy minimization
Model type detailsminimized average
AuthorsBanci, L. / Bertini, I. / Cantini, F. / Ciofi-Baffoni, S. / Gonnelli, L. / Mangani, S.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Solution Structure of Cox11, a Novel Type of {beta}-Immunoglobulin-like Fold Involved in CuB Site Formation of Cytochrome c Oxidase.
Authors: Banci, L. / Bertini, I. / Cantini, F. / Ciofi-Baffoni, S. / Gonnelli, L. / Mangani, S.
History
DepositionMar 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 / 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 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: Cytochrome C oxidase assembly protein ctaG


Theoretical massNumber of molelcules
Total (without water)18,3881
Polymers18,3881
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 Cytochrome C oxidase assembly protein ctaG / COX11


Mass: 18388.088 Da / Num. of mol.: 1 / Fragment: C-terminal soluble domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Gene: CTAG, R00908, SMC00012 / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92RG6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D NOESY
1232D TOCSY
1313D 15N-separated NOESY
141HNHA
1523D 13C-separated NOESY
16213C (H)CCH-TOCSY
172CBCA(CO)NH
182CBCANH
192HNCO
1102HN(CA)CO
NMR detailsText: This structure was determined using 3D heteronuclear techniques. The 500 MHz spectrometer was equipped with a triple resonance cryoprobe. All the triple resonance (TXI 5-mm) probes used were ...Text: This structure was determined using 3D heteronuclear techniques. The 500 MHz spectrometer was equipped with a triple resonance cryoprobe. All the triple resonance (TXI 5-mm) probes used were equipped with Pulsed Field Gradients along the z-axis

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM apoCox11 U-15N; 5mM DTT; 20 mM phosphate buffer NA90% H2O/10% D2O
21 mM apoCox11 U-95% 13C,U-98% 15N; 5 mM DTT; 20 mM phosphate buffer NA90% H2O/10% D2O
32 mM unlabelled apoCox11; 5 mM DTT; 20 mM phosphate buffer NA90% H2O/10% D2O
Sample conditionsIonic strength: 20 mM phosphate buffer / pH: 7 / 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 AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE5003

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Processing

NMR software
NameVersionClassification
XwinNMRcollection
XEASY1.3data analysis
DYANA1.5structure solution
CYANA1structure solution
Amber5refinement
RefinementMethod: torsion angle dynamics, simulated annealing, restrained energy minimization
Software ordinal: 1
Details: the structures were based on a total of 2867 meaningful distance constraints, 130 dihedral angle restraints
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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