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- PDB-1l6u: NMR STRUCTURE OF OXIDIZED ADRENODOXIN -

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Basic information

Entry
Database: PDB / ID: 1l6u
TitleNMR STRUCTURE OF OXIDIZED ADRENODOXIN
ComponentsAdrenodoxin 1
KeywordsELECTRON TRANSPORT / [2Fe-2S]-cluster / primary interaction domain (helix from Asp72-Asp79) / (alpha-beta)-Protein / 5 Helices / 5 beta strands
Function / homology
Function and homology information


Mitochondrial iron-sulfur cluster biogenesis / Pregnenolone biosynthesis / Electron transport from NADPH to Ferredoxin / Endogenous sterols / Protein lipoylation / hormone biosynthetic process / P450-containing electron transport chain / steroid biosynthetic process / cholesterol metabolic process / cellular response to forskolin ...Mitochondrial iron-sulfur cluster biogenesis / Pregnenolone biosynthesis / Electron transport from NADPH to Ferredoxin / Endogenous sterols / Protein lipoylation / hormone biosynthetic process / P450-containing electron transport chain / steroid biosynthetic process / cholesterol metabolic process / cellular response to forskolin / cellular response to cAMP / respiratory electron transport chain / electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / mitochondrial matrix / protein homodimerization activity / mitochondrion / metal ion binding
Similarity search - Function
Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) ...Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Adrenodoxin, mitochondrial
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsBeilke, D. / Weiss, R. / Lohr, F. / Pristovsek, P. / Hannemann, F. / Bernhardt, R. / Rueterjans, H.
Citation
Journal: Biochemistry / Year: 2002
Title: A new electron transport mechanism in mitochondrial steroid hydroxylase systems based on structural changes upon the reduction of adrenodoxin.
Authors: Beilke, D. / Weiss, R. / Lohr, F. / Pristovsek, P. / Hannemann, F. / Bernhardt, R. / Ruterjans, H.
#1: Journal: Structure / Year: 1998
Title: NEW ASPECTS OF ELECTRON TRANSFER REVEALED BY THE CRYSTAL STRUCTURE OF A TRUNCATED BOVINE ADRENODOXIN, ADX(4-108)
Authors: Muller, A. / Muller, J.J. / Muller, Y.A. / Uhlmann, H. / Bernhardt, R. / Heinemann, U.
History
DepositionMar 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Feb 5, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 2.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adrenodoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2382
Polymers14,0621
Non-polymers1761
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area250 Å2
ΔGint-17 kcal/mol
Surface area6510 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Adrenodoxin 1 / Adrenal ferredoxin / Hepato-ferredoxin


Mass: 14061.761 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Organ: adrenal gland / Production host: Escherichia coli (E. coli) / References: UniProt: P00257
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

DetailsContents: 2-3mM Adrenodoxin 15N,13C, 50 mM phosphate buffer, 50mM NaCl, 10% D2O, 0.04% NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100 mM salt / pH: 7.4 / Pressure: 1 atm / Temperature: 300 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 DMXBrukerDMX6001
Bruker DMXBrukerDMX5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.1Brukerprocessing
DYANA1.5Guentertstructure solution
nmr2st1Pristovsekdata analysis
DYANA1.5Guentertrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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