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- PDB-1cje: ADRENODOXIN FROM BOVINE -

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Basic information

Entry
Database: PDB / ID: 1cje
TitleADRENODOXIN FROM BOVINE
ComponentsADRENODOXIN
KeywordsELECTRON TRANSPORT / ELECTRON TRANSPORT PROTEIN / IRON SULFUR PROTEIN / 2FE-2S FERREDOXIN
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 / respiratory electron transport chain ...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 / 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 (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
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.
History
DepositionApr 12, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 21, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 27, 2019Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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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
Polymers55,8994
Non-polymers7034
Water2,378132
1
A: ADRENODOXIN
B: ADRENODOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3014
Polymers27,9492
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
Polymers27,9492
Non-polymers3522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
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-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.628402, -0.777877, 0.004196), (-0.777772, -0.628392, -0.013932), (0.013474, 0.005491, -0.999894)-3.951, -7.397, 50.552
2given(-0.997488, -0.043391, -0.055993), (-0.070739, 0.65197, 0.754938), (0.003749, 0.757002, -0.653402)-11.303, -11.739, 27.095
3given(-0.421366, -0.622282, -0.659709), (0.906878, -0.285346, -0.310079), (0.004711, -0.728933, 0.684569)0.712, 10.084, 22.972

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Components

#1: Protein
ADRENODOXIN


Mass: 13974.683 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH FE2/S2 (INORGANIC) CLUSTER / Source: (gene. exp.) Bos taurus (cattle) / Plasmid: PKK223-3 / 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 / Source method: obtained synthetically / Formula: Fe2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
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 Å3/Da / Density % sol: 51 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common 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: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 17191 / % possible obs: 92 % / Redundancy: 3.8 % / Biso Wilson estimate: 44.2 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 27
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.9 / % possible all: 57.4
Reflection
*PLUS
Num. obs: 17178 / Num. measured all: 66064
Reflection shell
*PLUS
% possible obs: 57 % / Rmerge(I) obs: 0.293

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AYF

1ayf


Resolution: 2.5→40 Å / Rfactor Rfree error: 0.008 / Data cutoff high rms absF: 385760.48 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.298 1646 10.4 %RANDOM
Rwork0.233 ---
obs-15878 84.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.1 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 44.5 Å2
Baniso -1Baniso -2Baniso -3
1-16.64 Å20 Å2-3.78 Å2
2---12.42 Å20 Å2
3----3.22 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å / Luzzati d res low obs: 8 Å / Luzzati sigma a obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3266 0 16 132 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
X-RAY DIFFRACTIONc_scbond_it4.152
X-RAY DIFFRACTIONc_scangle_it5.262.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.355 153 10.7 %
Rwork0.285 1279 -
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
Refinement
*PLUS
Lowest resolution: 8 Å / Rfactor Rfree: 0.311 / Rfactor Rwork: 0.235
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 44.4 Å2
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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