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- PDB-1cje: ADRENODOXIN FROM BOVINE -

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Entry
Database: PDB / ID: 1cje
TitleADRENODOXIN FROM BOVINE
ComponentsADRENODOXINAdrenal ferredoxin
KeywordsELECTRON TRANSPORT / ELECTRON TRANSPORT PROTEIN / IRON SULFUR PROTEIN / 2FE-2S FERREDOXIN
Function / homology2Fe-2S ferredoxin-type iron-sulfur binding domain / Endogenous sterols / Mitochondrial iron-sulfur cluster biogenesis / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / Adrenodoxin family, iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / 2Fe-2S ferredoxin-like superfamily / Adrenodoxin, iron-sulphur binding site / Beta-grasp domain superfamily / Adrenodoxin ...2Fe-2S ferredoxin-type iron-sulfur binding domain / Endogenous sterols / Mitochondrial iron-sulfur cluster biogenesis / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / Adrenodoxin family, iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / 2Fe-2S ferredoxin-like superfamily / Adrenodoxin, iron-sulphur binding site / Beta-grasp domain superfamily / Adrenodoxin / Pregnenolone biosynthesis / Electron transport from NADPH to Ferredoxin / hormone biosynthetic process / steroid biosynthetic process / cellular response to forskolin / cholesterol metabolic process / 2 iron, 2 sulfur cluster binding / cellular response to cAMP / oxidation-reduction process / protein C-terminus binding / mitochondrial matrix / electron transfer activity / protein homodimerization activity / mitochondrion / metal ion binding / Adrenodoxin, mitochondrial
Function and homology information
Specimen sourceBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 2.5 Å resolution
AuthorsPikuleva, I.A. / Tesh, K. / Waterman, M.R. / Kim, Y.
Citation
Journal: Arch.Biochem.Biophys. / Year: 2000
Title: The tertiary structure of full-length bovine adrenodoxin suggests functional dimers.
Authors: Pikuleva, I.A. / Tesh, K. / Waterman, M.R. / Kim, Y.
#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.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1985
Title: Molecular Cloning and Amino Acid Sequence of the Precursor Form of Bovine Adrenodoxin: Evidence for a Previously Unidentified Cooh-Terminal Peptide
Authors: Okamura, T. / John, M.E. / Zuber, M.X. / Simpson, E.R. / Waterman, M.R.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 12, 1999 / Release: Jan 21, 2000
RevisionDateData content typeGroupProviderType
1.0Jan 21, 2000Structure modelrepositoryInitial release
1.1Apr 26, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADRENODOXIN
B: ADRENODOXIN
C: ADRENODOXIN
D: ADRENODOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6028
Polyers55,8994
Non-polymers7034
Water2,378132
1
A: ADRENODOXIN
B: ADRENODOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3014
Polyers27,9492
Non-polymers3522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: ADRENODOXIN
D: ADRENODOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3014
Polyers27,9492
Non-polymers3522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)59.443, 77.025, 59.681
Angle α, β, γ (deg.)90.00, 94.83, 90.00
Int Tables number4
Space group name H-MP 1 21 1

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Components

#1: Protein/peptide
ADRENODOXIN / Adrenal ferredoxin


Mass: 13974.683 Da / Num. of mol.: 4 / Details: COMPLEXED WITH FE2/S2 (INORGANIC) CLUSTER / Source: (gene. exp.) Bos taurus (cattle) / Genus: Bos / Plasmid name: PKK223-3 / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / Strain (production host): D1210 / References: UniProt: P00257
#2: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Formula: Fe2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Formula: H2O / Water
Compound detailsTHE MATURE ADRENODOXIN IS GENERATED FROM THE ADREDOXIN PRECURSOR (ADX_BOVIN: P00257) BY CLEAVING ...THE MATURE ADRENODOXIN IS GENERATED FROM THE ADREDOXIN PRECURSOR (ADX_BOVIN: P00257) BY CLEAVING OFF THE FIRST 58 AMINO ACIDS AT THE N-TERMINUS. THIS PDB ENTRY CONTAINS THE STRUCTURE OF THE MATURED ADREDOXIN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 / Density percent sol: 51 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temp: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
123 mg/mlprotein1drop
230 %PEG40001reservoir
30.1 MNa HEPES1reservoir
4150 mM1reservoirMgCl2
540 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 12 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Details: MIRRORS / Detector: IMAGE PLATE / Collection date: Apr 1, 1996
RadiationMonochromator: NI FILTER / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 44.2 Å2 / D resolution high: 2.5 Å / D resolution low: 4 Å / Number obs: 17191 / Rmerge I obs: 0.076 / NetI over sigmaI: 27 / Redundancy: 3.8 % / Percent possible obs: 92
Reflection shellRmerge I obs: 0.29 / Highest resolution: 2.5 Å / Lowest resolution: 2.59 Å / MeanI over sigI obs: 3.9 / Redundancy: 3.1 % / Percent possible all: 57.4
Reflection
*PLUS
Number obs: 17178 / Number measured all: 66064
Reflection shell
*PLUS
Percent possible obs: 57 / Rmerge I obs: 0.293

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AYF
Details: BULK SOLVENT MODEL USED / R Free selection details: RANDOM / Data cutoff high rms absF: 385760.48 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 2
Solvent computationSolvent model details: FLAT MODEL / Solvent model param bsol: 59.1 / Solvent model param ksol: 0.34
Displacement parametersB iso mean: 44.5 Å2 / Aniso B11: 16.64 Å2 / Aniso B12: 0 Å2 / Aniso B13: -3.78 Å2 / Aniso B22: -12.42 Å2 / Aniso B23: 0 Å2 / Aniso B33: -3.22 Å2
Least-squares processR factor R free: 0.298 / R factor R free error: 0.008 / R factor R work: 0.233 / Highest resolution: 2.5 Å / Lowest resolution: 4 Å / Number reflection R free: 1646 / Number reflection obs: 15878 / Percent reflection R free: 10.4 / Percent reflection obs: 84.9
Refine analyzeLuzzati coordinate error obs: 0.34 Å / Luzzati d res low obs: 8 Å / Luzzati sigma a obs: 0.33 Å
Refine hist #LASTHighest resolution: 2.5 Å / Lowest resolution: 4 Å
Number of atoms included #LASTProtein: 3266 / Nucleic acid: 0 / Ligand: 16 / Solvent: 132 / Total: 3414
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.996
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.54
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.521.5
X-RAY DIFFRACTIONc_mcangle_it4.22.0
X-RAY DIFFRACTIONc_scbond_it4.152.0
X-RAY DIFFRACTIONc_scangle_it5.262.5
Refine LS shellHighest resolution: 2.5 Å / R factor R free: 0.355 / R factor R free error: 0.03 / R factor R work: 0.285 / Lowest resolution: 2.66 Å / Number reflection R free: 153 / Number reflection R work: 1279 / Total number of bins used: 6 / Percent reflection R free: 10.7 / Percent reflection obs: 46.5
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3FES.PARMFES.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Displacement parameters
*PLUS
B iso mean: 44.4 Å2
Least-squares process
*PLUS
R factor R free: 0.311 / R factor R work: 0.235 / Lowest resolution: 8 Å
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.202
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.54

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