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

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Basic information

Entry
Database: PDB / ID: 1ayf
TitleBOVINE ADRENODOXIN (OXIDIZED)
ComponentsADRENODOXINAdrenal ferredoxin
KeywordsELECTRON TRANSPORT / [2FE-2S]FERREDOXIN / ADRENODOXIN
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 / rt:r-bta-2395516: / 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 / 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 3, 1997 / Release: Dec 30, 1998
RevisionDateData content typeGroupProviderType
1.0Dec 30, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance

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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
Polyers23,3222
Non-polymers4443
Water3,009167
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
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-MP 21 21 2
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/peptide ADRENODOXIN / Adrenal ferredoxin


Mass: 11661.205 Da / Num. of mol.: 2 / 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 / Formula: Fe2S2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Formula: C3H8O3 / Glycerol
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Formula: H2O / Water

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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

Crystal-ID: 1

IDConc.Common nameSol-IDChemical formula
120 mg/mlproteindrop
230 %(w/v)PEG4000reservoir
3100 mMTris-HClreservoir
410 %glycerolreservoir
5100 mMreservoirMgCl2

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.92
DetectorType: MARRESEARCH / Details: TOROIDAL MIRROR / Detector: IMAGE PLATE / Date: Mar 1, 1997
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
Rfree0.253191110 %RANDOM
Rwork0.195---
obs0.1931843199.9 %-
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. atoms15920141671773
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal target
p_bond_d0.0120.02
p_angle_d0.0150.02
p_angle_deg
p_planar_d
p_hb_or_metal_coord
p_mcbond_it2.083
p_mcangle_it2.8144
p_scbond_it2.9434
p_scangle_it4.1125
p_plane_restr0.02430.03
p_chiral_restr0.1280.15
p_singtor_nbd0.1850.3
p_multtor_nbd0.2620.3
p_xhyhbond_nbd00.3
p_xyhbond_nbd0.1890.3
p_planar_tor4.24
p_staggered_tor19.415
p_orthonormal_tor
p_transverse_tor29.415
p_special_tor015
Software
*PLUS
Name: CCP4 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.195

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