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- PDB-4fdh: Structure of human aldosterone synthase, CYP11B2, in complex with... -

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Basic information

Entry
Database: PDB / ID: 4fdh
TitleStructure of human aldosterone synthase, CYP11B2, in complex with fadrozole
ComponentsCytochrome P450 11B2, mitochondrial
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / cytochrome P450 / CYP11B2 / Aldosterone synthase / monooxygenase / heme protein / mineralocorticoid / inhibitor / mitochondria / membrane / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


corticosterone 18-monooxygenase / regulation of blood volume by renal aldosterone / Defective CYP11B2 causes CMO-1 deficiency / steroid 11beta-monooxygenase / steroid 11-beta-monooxygenase activity / mineralocorticoid biosynthetic process / corticosterone 18-monooxygenase activity / cortisol metabolic process / aldosterone biosynthetic process / cortisol biosynthetic process ...corticosterone 18-monooxygenase / regulation of blood volume by renal aldosterone / Defective CYP11B2 causes CMO-1 deficiency / steroid 11beta-monooxygenase / steroid 11-beta-monooxygenase activity / mineralocorticoid biosynthetic process / corticosterone 18-monooxygenase activity / cortisol metabolic process / aldosterone biosynthetic process / cortisol biosynthetic process / Mineralocorticoid biosynthesis / glucocorticoid biosynthetic process / Glucocorticoid biosynthesis / sodium ion homeostasis / sterol metabolic process / cellular response to potassium ion / C21-steroid hormone biosynthetic process / potassium ion homeostasis / steroid hydroxylase activity / cellular response to peptide hormone stimulus / Endogenous sterols / renal water homeostasis / cellular response to hormone stimulus / cholesterol metabolic process / mitochondrial inner membrane / iron ion binding / heme binding / mitochondrion
Similarity search - Function
Cytochrome P450, mitochondrial / : / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-0T3 / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 11B2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsStrushkevich, N. / Shen, L. / Tempel, W. / Arrowsmith, C. / Edwards, A. / Usanov, S.A. / Park, H.-W.
CitationJournal: Mol.Endocrinol. / Year: 2013
Title: Structural insights into aldosterone synthase substrate specificity and targeted inhibition.
Authors: Strushkevich, N. / Gilep, A.A. / Shen, L. / Arrowsmith, C.H. / Edwards, A.M. / Usanov, S.A. / Park, H.W.
History
DepositionMay 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_ref_seq_dif.details / _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: Cytochrome P450 11B2, mitochondrial
B: Cytochrome P450 11B2, mitochondrial
C: Cytochrome P450 11B2, mitochondrial
D: Cytochrome P450 11B2, mitochondrial
E: Cytochrome P450 11B2, mitochondrial
F: Cytochrome P450 11B2, mitochondrial
G: Cytochrome P450 11B2, mitochondrial
H: Cytochrome P450 11B2, mitochondrial
I: Cytochrome P450 11B2, mitochondrial
J: Cytochrome P450 11B2, mitochondrial
K: Cytochrome P450 11B2, mitochondrial
L: Cytochrome P450 11B2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)677,87136
Polymers667,79412
Non-polymers10,07724
Water2,288127
1
A: Cytochrome P450 11B2, mitochondrial
B: Cytochrome P450 11B2, mitochondrial
C: Cytochrome P450 11B2, mitochondrial
D: Cytochrome P450 11B2, mitochondrial
E: Cytochrome P450 11B2, mitochondrial
F: Cytochrome P450 11B2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)338,93618
Polymers333,8976
Non-polymers5,03912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19490 Å2
ΔGint-191 kcal/mol
Surface area108260 Å2
MethodPISA
2
G: Cytochrome P450 11B2, mitochondrial
H: Cytochrome P450 11B2, mitochondrial
I: Cytochrome P450 11B2, mitochondrial
J: Cytochrome P450 11B2, mitochondrial
K: Cytochrome P450 11B2, mitochondrial
L: Cytochrome P450 11B2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)338,93618
Polymers333,8976
Non-polymers5,03912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19870 Å2
ΔGint-188 kcal/mol
Surface area108310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.751, 199.086, 150.018
Angle α, β, γ (deg.)90.000, 112.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cytochrome P450 11B2, mitochondrial / Aldosterone synthase / ALDOS / Aldosterone-synthesizing enzyme / CYPXIB2 / Cytochrome P-450Aldo / ...Aldosterone synthase / ALDOS / Aldosterone-synthesizing enzyme / CYPXIB2 / Cytochrome P-450Aldo / Cytochrome P-450C18 / Steroid 18-hydroxylase


Mass: 55649.500 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Aldosterone synthase, CYP11B2 / Plasmid: pCW / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a
References: UniProt: P19099, steroid 11beta-monooxygenase, corticosterone 18-monooxygenase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-0T3 / 4-[(5R)-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-5-yl]benzonitrile / fadrozole


Mass: 223.273 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C14H13N3 / Comment: inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.69 Å3/Da / Density % sol: 54.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 12% PEG 4000, 0.1M Tris, pH 8.5, 0.2M Lithium sulfate, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.71→49.19 Å / Num. all: 188505 / Num. obs: 179030 / % possible obs: 98.99 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.5434
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allDiffraction-ID% possible all
2.71-2.863.240.0118568426406195.22
2.86-3.033.410.0118904226074199.42
3.03-3.243.580.0118833824645199.76
3.24-3.53.730.0118564922963199.89
3.5-3.833.780.0118008421174199.85
3.83-4.293.760.0117174419080199.74
4.29-4.953.720.0116266716856199.72
4.95-6.063.70.0115279614265199.73
6.06-8.573.660.0114044211051199.51
8.57-49.193.630.011217195991197.71

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.9data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→48.89 Å / Occupancy max: 1 / Occupancy min: 1
RfactorNum. reflection
Rfree0.29959 -
Rwork0.22441 -
obs0.22814 179030
Displacement parametersBiso max: 125.94 Å2 / Biso mean: 66.9869 Å2 / Biso min: 28.44 Å2
Refinement stepCycle: LAST / Resolution: 2.71→48.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms45228 0 720 127 46075

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