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

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Basic information

Entry
Database: PDB / ID: 4dvq
TitleStructure of human aldosterone synthase, CYP11B2, in complex with deoxycorticosterone
ComponentsCytochrome P450 11B2, mitochondrial
KeywordsOXIDOREDUCTASE / cytochrome P450 / CYP11B2 / Aldosterone synthase / monooxygenase / heme protein / mineralocorticoid / corticosteroid / mitochondria / membrane
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 / C21-steroid hormone biosynthetic process / steroid hydroxylase activity / potassium ion homeostasis / cellular response to potassium ion / 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
DESOXYCORTICOSTERONE / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 11B2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.49 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
DepositionFeb 23, 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_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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)680,02245
Polymers667,79412
Non-polymers12,22833
Water4,684260
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)340,15524
Polymers333,8976
Non-polymers6,25818
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24100 Å2
ΔGint-199 kcal/mol
Surface area106890 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)339,86721
Polymers333,8976
Non-polymers5,97015
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24520 Å2
ΔGint-188 kcal/mol
Surface area106590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.347, 199.629, 150.153
Angle α, β, γ (deg.)90.00, 112.18, 90.00
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-1CA / DESOXYCORTICOSTERONE / 4-PREGNEN-21-OL-3,20-DIONE / DOC / 21-HYDROXYPROGESTERONE


Mass: 330.461 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H30O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.8 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 298 K / pH: 8.5
Details: 6% PEG 4000, 0.1M Tris, pH 8.5, 0.2M Lithium sulfate, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
XDSdataset1001
11
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
XDSdataset
SYNCHROTRONCLSI 08ID-110.97949
Detector
TypeIDDetectorDate
XDSdataset
RAYONIX MX-3001CCDJan 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.49→48.55 Å / Num. obs: 245749 / % possible obs: 99.21 % / Redundancy: 4.24 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 12.7435
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.49-2.6240.94195.08
2.62-2.784.190.67199.79
2.78-2.984.240.4199.95
2.98-3.214.30.23199.97
3.21-3.524.330.13199.97
3.52-3.944.320.07199.97
3.94-4.554.310.04199.97
4.55-5.574.30.04199.98
5.57-7.874.280.03199.95
7.87-48.554.20.02199.51

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.9data scaling
MOLREPphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→48.07 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 1 / SU B: 10.859 / SU ML: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflection
Rfree0.263 12220 4.973 %
Rwork0.204 --
obs0.207 245706 99.2 %
Solvent computationSolvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 45.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.336 Å20 Å20.579 Å2
2--0.565 Å20 Å2
3----0.464 Å2
Refinement stepCycle: LAST / Resolution: 2.49→48.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms45085 0 849 260 46194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0247254
X-RAY DIFFRACTIONr_bond_other_d0.0010.0232605
X-RAY DIFFRACTIONr_angle_refined_deg1.3192.00564368
X-RAY DIFFRACTIONr_angle_other_deg0.886378990
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.89955526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.08122.8632183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.844157953
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4815384
X-RAY DIFFRACTIONr_chiral_restr0.0710.27000
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02151416
X-RAY DIFFRACTIONr_gen_planes_other0.0020.029936
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7391.527816
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.452244974
X-RAY DIFFRACTIONr_scbond_it2.295319403
X-RAY DIFFRACTIONr_scangle_it3.7844.519341
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.49→2.56 Å
RfactorNum. reflection% reflection
Rfree0.378 838 -
Rwork0.328 15486 -
obs--90.31 %

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