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- PDB-1ayf: BOVINE ADRENODOXIN (OXIDIZED) -

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Basic information

Entry
Database: PDB / ID: 1ayf
TitleBOVINE ADRENODOXIN (OXIDIZED)
ComponentsADRENODOXIN
KeywordsELECTRON TRANSPORT / [2FE-2S]FERREDOXIN / ADRENODOXIN
Function / homology
Function and homology information


Mitochondrial iron-sulfur cluster biogenesis / Pregnenolone biosynthesis / Endogenous sterols / Electron transport from NADPH to Ferredoxin / hormone biosynthetic process / P450-containing electron transport chain / steroid biosynthetic process / respiratory electron transport chain / cholesterol metabolic process / electron transport chain ...Mitochondrial iron-sulfur cluster biogenesis / Pregnenolone biosynthesis / Endogenous sterols / Electron transport from NADPH to Ferredoxin / hormone biosynthetic process / P450-containing electron transport chain / steroid biosynthetic process / respiratory electron transport chain / cholesterol metabolic process / 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 / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsMueller, A. / Mueller, J.J. / Heinemann, U.
CitationJournal: 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
DepositionNov 3, 1997Processing site: BNL
Revision 1.0Dec 30, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7665
Polymers23,3222
Non-polymers4443
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.180, 78.340, 60.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-603-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.328, 0.9268, 0.183), (0.9442, -0.3158, -0.09306), (-0.02844, 0.2033, -0.9787)
Vector: -0.2346, 1.556, 13.06)

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Components

#1: Protein ADRENODOXIN


Mass: 11661.205 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Organ: ADRENAL GLAND / Organelle: MITOCHONDRION / Plasmid: PKKHC, PMIXT / Production host: Escherichia coli (E. coli) / Strain (production host): HB 101 / References: UniProt: P00257
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O

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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: 2.24 Å3/Da / Density % sol: 44 %
Crystal growpH: 7.4
Details: PROTEIN WAS CRYSTALLIZED FROM 30% PEG 4000, 10% GLYCEROL, 100 MM TRIS, PH 7.4, 100MM MGCL2, 20 MG/ML PROTEIN
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.3 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
230 %(w/v)PEG40001reservoir
3100 mMTris-HCl1reservoir
410 %glycerol1reservoir
5100 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1997 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.75→11 Å / Num. obs: 21775 / % possible obs: 99.9 % / Redundancy: 5 % / Biso Wilson estimate: 19.2 Å2 / Rsym value: 0.044 / Net I/σ(I): 30.956
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 7.74 / Rsym value: 0.204 / % possible all: 99.1
Reflection
*PLUS
Lowest resolution: 10 Å / Rmerge(I) obs: 0.044 / Biso Wilson estimate: 16.4 Å2
Reflection shell
*PLUS
Redundancy: 5 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 7.7

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Processing

Software
NameClassification
DMmodel building
HEAVYmodel building
MLPHAREphasing
CCP4refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
HEAVYphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→11 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1911 10 %RANDOM
Rwork0.195 ---
obs0.193 18431 99.9 %-
all-18431 --
Displacement parametersBiso mean: 23.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 11 Å
Refinement stepCycle: LAST / Resolution: 1.85→11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1592 0 14 167 1773
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0150.02
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.083
X-RAY DIFFRACTIONp_mcangle_it2.8144
X-RAY DIFFRACTIONp_scbond_it2.9434
X-RAY DIFFRACTIONp_scangle_it4.1125
X-RAY DIFFRACTIONp_plane_restr0.02430.03
X-RAY DIFFRACTIONp_chiral_restr0.1280.15
X-RAY DIFFRACTIONp_singtor_nbd0.1850.3
X-RAY DIFFRACTIONp_multtor_nbd0.2620.3
X-RAY DIFFRACTIONp_xhyhbond_nbd00.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.1890.3
X-RAY DIFFRACTIONp_planar_tor4.24
X-RAY DIFFRACTIONp_staggered_tor19.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.415
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: CCP4 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS

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