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- PDB-7e7f: Human CYP11B1 mutant in complex with metyrapone -

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Basic information

Entry
Database: PDB / ID: 7e7f
TitleHuman CYP11B1 mutant in complex with metyrapone
ComponentsCytochrome P450 11B1, mitochondrial
KeywordsOXIDOREDUCTASE / P450
Function / homology
Function and homology information


Defective CYP11B1 causes AH4 / steroid 11beta-monooxygenase / steroid 11-beta-monooxygenase activity / corticosterone 18-monooxygenase activity / cortisol metabolic process / aldosterone biosynthetic process / cortisol biosynthetic process / glucocorticoid biosynthetic process / Glucocorticoid biosynthesis / sterol metabolic process ...Defective CYP11B1 causes AH4 / steroid 11beta-monooxygenase / steroid 11-beta-monooxygenase activity / corticosterone 18-monooxygenase activity / cortisol metabolic process / aldosterone biosynthetic process / cortisol biosynthetic process / glucocorticoid biosynthetic process / Glucocorticoid biosynthesis / sterol metabolic process / cellular response to potassium ion / C21-steroid hormone biosynthetic process / cellular response to peptide hormone stimulus / Endogenous sterols / cellular response to hormone stimulus / cholesterol metabolic process / regulation of blood pressure / glucose homeostasis / mitochondrial inner membrane / immune response / iron ion binding / heme binding / mitochondrion
Similarity search - Function
Cytochrome P450, mitochondrial / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
CHOLIC ACID / PROTOPORPHYRIN IX CONTAINING FE / METYRAPONE / Cytochrome P450 11B1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
Model detailsMitocondrial cytochrome P450 11B1
AuthorsMukai, K. / Sugimoto, H. / Reiko, S. / Matsuura, T. / Hishiki, T. / Kagawa, N.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)26461387 Japan
Japan Society for the Promotion of Science (JSPS)17K09890 Japan
CitationJournal: Curr Res Struct Biol / Year: 2021
Title: Spatially restricted substrate-binding site of cortisol-synthesizing CYP11B1 limits multiple hydroxylations and hinders aldosterone synthesis.
Authors: Mukai, K. / Sugimoto, H. / Kamiya, K. / Suzuki, R. / Matsuura, T. / Hishiki, T. / Shimada, H. / Shiro, Y. / Suematsu, M. / Kagawa, N.
History
DepositionFeb 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 5, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 11B1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6657
Polymers55,8211
Non-polymers1,8446
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-18 kcal/mol
Surface area21690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.180, 84.600, 85.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytochrome P450 11B1, mitochondrial / CYPXIB1 / Cytochrome P-450c11 / Cytochrome P450C11 / Steroid 11-beta-hydroxylase / CYP11B1


Mass: 55821.336 Da / Num. of mol.: 1 / Fragment: heme binding protein / Mutation: W49R,L50N,W53R,W56R,L244N,W247N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP11B1, S11BH / Plasmid: pET-17b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P15538, steroid 11beta-monooxygenase

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Non-polymers , 5 types, 424 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-MYT / METYRAPONE / Metyrapone


Mass: 226.274 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14N2O / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, inhibitor*YM
#4: Chemical ChemComp-CHD / CHOLIC ACID / Cholic acid


Mass: 408.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H40O5
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.44 Å3/Da / Density % sol: 49.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 100mM potassium phosphate, 150mM NaCl, 4% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 14, 2018 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→47.02 Å / Num. obs: 105301 / % possible obs: 97.6 % / Redundancy: 17.249 % / Biso Wilson estimate: 30.218 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.046 / Χ2: 1.036 / Net I/σ(I): 29.34 / Num. measured all: 1816384 / Scaling rejects: 2235
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.4-1.4814.3941.1342.1621270716414147770.7631.17490
1.48-1.5918.0520.5825.1830891217469171120.9540.59998
1.59-1.7117.6350.3029.6924876614342141060.9870.31198.4
1.71-1.8818.250.15418.5626307414581144150.9970.15898.9
1.88-2.117.6230.0833.1121921712543124390.9990.08299.2
2.1-2.4217.8720.05251.2619759811106110560.9990.05399.5
2.42-2.9617.7420.0466.171692039557953710.04199.8
2.96-4.1816.8420.03378.981268367537753110.03499.9
4.18-47.0216.190.03383.2170071433543280.9990.03499.8

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Processing

Software
NameVersionClassification
XSCALENov 11,2017data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
ARP/wARP7.6data reduction
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DVQ

4dvq


Resolution: 1.4→47.02 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.969 / SU ML: 0.034 / SU R Cruickshank DPI: 0.0544 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1634 5230 5 %RANDOM
Rwork0.1397 ---
obs0.1409 100071 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.91 Å2 / Biso mean: 28.886 Å2 / Biso min: 15.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2--0.58 Å2-0 Å2
3----0.34 Å2
Refinement stepCycle: final / Resolution: 1.4→47.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3812 0 130 418 4360
Biso mean--27.88 41.74 -
Num. residues----472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134136
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173888
X-RAY DIFFRACTIONr_angle_refined_deg1.531.6615649
X-RAY DIFFRACTIONr_angle_other_deg1.4051.5729004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9895494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.19820.377239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91115697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.241542
X-RAY DIFFRACTIONr_chiral_restr0.0820.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024571
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02941
X-RAY DIFFRACTIONr_rigid_bond_restr4.50138024
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 331 -
Rwork0.288 6328 -
all-6659 -
obs--84.08 %

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