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- PDB-7m8i: Human CYP11B2 and human adrenodoxin in complex with fadrozole -

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Basic information

Entry
Database: PDB / ID: 7m8i
TitleHuman CYP11B2 and human adrenodoxin in complex with fadrozole
ComponentsAdrenodoxin, Cytochrome P450 11B2, mitochondrial fusion enzymeAdrenal ferredoxin
KeywordsOXIDOREDUCTASE / aldosterone synthase / CYP11B2 / electron transfer
Function / homology
Function and homology information


corticosterone 18-monooxygenase / regulation of blood volume by renal aldosterone / Electron transport from NADPH to Ferredoxin / Defective CYP11B2 causes CMO-1 deficiency / Defective CYP11A1 causes AICSR / mineralocorticoid biosynthetic process / steroid 11beta-monooxygenase / steroid 11-beta-monooxygenase activity / corticosterone 18-monooxygenase activity / cortisol metabolic process ...corticosterone 18-monooxygenase / regulation of blood volume by renal aldosterone / Electron transport from NADPH to Ferredoxin / Defective CYP11B2 causes CMO-1 deficiency / Defective CYP11A1 causes AICSR / mineralocorticoid biosynthetic process / steroid 11beta-monooxygenase / steroid 11-beta-monooxygenase activity / corticosterone 18-monooxygenase activity / cortisol metabolic process / aldosterone biosynthetic process / cortisol biosynthetic process / Mineralocorticoid biosynthesis / glucocorticoid biosynthetic process / Mitochondrial iron-sulfur cluster biogenesis / hormone biosynthetic process / P450-containing electron transport chain / Glucocorticoid biosynthesis / sodium ion homeostasis / sterol metabolic process / cellular response to potassium ion / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / steroid biosynthetic process / potassium ion homeostasis / renal water homeostasis / steroid hydroxylase activity / cellular response to peptide hormone stimulus / Endogenous sterols / cellular response to cAMP / cellular response to forskolin / cellular response to hormone stimulus / cholesterol metabolic process / electron transport chain / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / electron transfer activity / mitochondrial matrix / iron ion binding / heme binding / mitochondrion
Similarity search - Function
Cytochrome P450, mitochondrial / Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / 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 / Cytochrome P450, conserved site ...Cytochrome P450, mitochondrial / Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / 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 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
Chem-0T3 / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / Adrenodoxin, mitochondrial / Cytochrome P450 11B2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsScott, E.E. / Brixius-Anderko, S.
Funding support United States, 1items
OrganizationGrant numberCountry
American Heart Association19POST34430199 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural and functional insights into aldosterone synthase interaction with its redox partner protein adrenodoxin.
Authors: Brixius-Anderko, S. / Scott, E.E.
History
DepositionMar 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 14, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adrenodoxin, Cytochrome P450 11B2, mitochondrial fusion enzyme
B: Adrenodoxin, Cytochrome P450 11B2, mitochondrial fusion enzyme
C: Adrenodoxin, Cytochrome P450 11B2, mitochondrial fusion enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,02712
Polymers207,9803
Non-polymers3,0479
Water181
1
A: Adrenodoxin, Cytochrome P450 11B2, mitochondrial fusion enzyme
B: Adrenodoxin, Cytochrome P450 11B2, mitochondrial fusion enzyme
C: Adrenodoxin, Cytochrome P450 11B2, mitochondrial fusion enzyme
hetero molecules

A: Adrenodoxin, Cytochrome P450 11B2, mitochondrial fusion enzyme
B: Adrenodoxin, Cytochrome P450 11B2, mitochondrial fusion enzyme
C: Adrenodoxin, Cytochrome P450 11B2, mitochondrial fusion enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)422,05424
Polymers415,9616
Non-polymers6,09318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area20750 Å2
ΔGint-282 kcal/mol
Surface area130010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.579, 208.700, 124.919
Angle α, β, γ (deg.)90.000, 114.073, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Adrenodoxin, Cytochrome P450 11B2, mitochondrial fusion enzyme / Adrenal ferredoxin / Adrenal ferredoxin / Ferredoxin-1 / Hepatoredoxin / Aldosterone synthase / ALDOS / Aldosterone- ...Adrenal ferredoxin / Ferredoxin-1 / Hepatoredoxin / Aldosterone synthase / ALDOS / Aldosterone-synthesizing enzyme / CYPXIB2 / Corticosterone 18-monooxygenase / CYP11B2 / Cytochrome P-450Aldo / Cytochrome P-450C18 / Steroid 11-beta-hydroxylase / Steroid 18-hydroxylase


Mass: 69326.820 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FDX1, ADX, CYP11B2 / Plasmid: pCWORI+ / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha
References: UniProt: P10109, UniProt: P19099, corticosterone 18-monooxygenase, steroid 11beta-monooxygenase
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Fe2S2
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-0T3 / 4-[(5R)-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-5-yl]benzonitrile / fadrozole / Fadrozole


Mass: 223.273 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H13N3 / Comment: inhibitor*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.02 Å3/Da / Density % sol: 69.42 % / Description: Plate
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M lithium sulfate 0.1 M Tris hydrochloride, pH 8.5 30% PEG 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.933→50 Å / Num. obs: 69937 / % possible obs: 100 % / Redundancy: 7.7 % / Biso Wilson estimate: 59.2 Å2 / CC1/2: 0.991 / Rpim(I) all: 0.073 / Net I/σ(I): 11.06
Reflection shellResolution: 2.933→2.99 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3458 / CC1/2: 0.56 / Rpim(I) all: 0.612

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FDH, 3P1M

4fdh

3p1m


Resolution: 2.94→48.16 Å / SU ML: 0.3866 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.5257
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2439 2000 3.13 %
Rwork0.2096 61799 -
obs0.2107 63799 90.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.62 Å2
Refinement stepCycle: LAST / Resolution: 2.94→48.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13474 0 192 1 13667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012314013
X-RAY DIFFRACTIONf_angle_d1.160619031
X-RAY DIFFRACTIONf_chiral_restr0.06372088
X-RAY DIFFRACTIONf_plane_restr0.0072430
X-RAY DIFFRACTIONf_dihedral_angle_d27.23535178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.94-3.010.3296800.31132476X-RAY DIFFRACTION51.34
3.01-3.090.36311020.29623140X-RAY DIFFRACTION65.18
3.09-3.180.35871190.28853690X-RAY DIFFRACTION75.73
3.18-3.280.34461330.27554123X-RAY DIFFRACTION85.86
3.28-3.40.32491500.25714632X-RAY DIFFRACTION95.18
3.4-3.530.27261560.24024828X-RAY DIFFRACTION99.64
3.53-3.690.26471580.22974855X-RAY DIFFRACTION99.94
3.69-3.890.2561570.21314844X-RAY DIFFRACTION100
3.89-4.130.22191560.19064846X-RAY DIFFRACTION100
4.13-4.450.23681580.17514872X-RAY DIFFRACTION100
4.45-4.90.19511560.16984831X-RAY DIFFRACTION99.98
4.9-5.610.23461580.19284870X-RAY DIFFRACTION100
5.61-7.060.2411580.22574883X-RAY DIFFRACTION100

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