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- PDB-1j6q: Solution structure and characterization of the heme chaperone CcmE -

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Basic information

Entry
Database: PDB / ID: 1j6q
TitleSolution structure and characterization of the heme chaperone CcmE
Componentscytochrome c maturation protein E
KeywordsCHAPERONE / all-beta protein / heme delivery / cytochrome c maturation / OB-(oligonucleotide binding)fold
Function / homology
Function and homology information


cytochrome complex assembly / heme binding / metal ion binding / plasma membrane
Similarity search - Function
CcmE/CycJ protein / CcmE-like superfamily / CcmE / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Cytochrome c-type biogenesis protein CcmE / Cytochrome c-type biogenesis protein CcmE
Similarity search - Component
Biological speciesShewanella putrefaciens (bacteria)
MethodSOLUTION NMR / simulated annealing, torsion angle dyanamics, restrained energy minimization
Model type detailsminimized average
AuthorsArnesano, F. / Banci, L. / Barker, P.D. / Bertini, I. / Rosato, A. / Su, X.C. / Viezzoli, M.S.
CitationJournal: Biochemistry / Year: 2002
Title: Solution structure and characterization of the heme chaperone CcmE
Authors: Arnesano, F. / Banci, L. / Barker, P.D. / Bertini, I. / Rosato, A. / Su, X.C. / Viezzoli, M.S.
History
DepositionApr 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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 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 maturation protein E


Theoretical massNumber of molelcules
Total (without water)14,7141
Polymers14,7141
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)1 / -
RepresentativeModel #1minimized average structure

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Components

#1: Protein cytochrome c maturation protein E


Mass: 14714.397 Da / Num. of mol.: 1 / Fragment: water soluble domain of CcmE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella putrefaciens (bacteria) / Gene: ccmE / Plasmid: pPB10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold(DE3) / References: UniProt: O52690, UniProt: Q8EK44*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1313D 13C-separated NOESY
1413D 15N-separated NOESY
151HNHA
161HNCO
171HNHB
181CBCANH
191CC(CO)NH
1101CBCA(CO)NH
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy on 13C and 15N double labeled apoCcmE.

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Sample preparation

DetailsContents: 2.0 mM apoCcmE, 20 mM phosphate, 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 20 mM phosphate / pH: 7.0 / Pressure: 1 atm / 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 spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukerprocessing
XEASY1.3Xia, Bartelsdata analysis
DYANA1.5Gunter, Mumenthaler, Wuthrichstructure solution
CORMABorgias, Thomas, Jamesiterative matrix relaxation
Amber5Pearlman, Case, Caldwell, Ross, Cheatham, Ferguson, Seibel, Singh, Weiner, Kollmanrefinement
RefinementMethod: simulated annealing, torsion angle dyanamics, restrained energy minimization
Software ordinal: 1
Details: 1866 meaningful NOEs and 89 dihedral angle constraints.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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