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- PDB-8sbi: Crystal structure of human sterol 14 alpha-demethylase (CYP51) in... -

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Basic information

Entry
Database: PDB / ID: 8sbi
TitleCrystal structure of human sterol 14 alpha-demethylase (CYP51) in the ligand-free state
ComponentsLanosterol 14-alpha demethylase
KeywordsOXIDOREDUCTASE / MONOOXYGENASE / CYTOCHROME P450 / ENDOPLASMIC RETICULUM / STEROL BIOSYNTHESIS
Function / homology
Function and homology information


sterol 14alpha-demethylase / sterol 14-demethylase activity / negative regulation of amyloid-beta clearance / sterol metabolic process / Cholesterol biosynthesis / EGR2 and SOX10-mediated initiation of Schwann cell myelination / steroid biosynthetic process / cholesterol biosynthetic process / negative regulation of protein secretion / Endogenous sterols ...sterol 14alpha-demethylase / sterol 14-demethylase activity / negative regulation of amyloid-beta clearance / sterol metabolic process / Cholesterol biosynthesis / EGR2 and SOX10-mediated initiation of Schwann cell myelination / steroid biosynthetic process / cholesterol biosynthetic process / negative regulation of protein secretion / Endogenous sterols / Activation of gene expression by SREBF (SREBP) / negative regulation of protein catabolic process / oxidoreductase activity / iron ion binding / heme binding / endoplasmic reticulum membrane / membrane
Similarity search - Function
: / Cytochrome P450, E-class, group IV / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Lanosterol 14-alpha demethylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsHargrove, T.Y. / Wawrzak, Z. / Lepesheva, G.I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM067871 United States
CitationJournal: To Be Published
Title: Structural dynamics of sterol 14 alpha demethylases upon catalysis
Authors: Hargrove, T.Y. / Wawrzak, Z. / Lepesheva, G.I.
History
DepositionApr 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lanosterol 14-alpha demethylase
B: Lanosterol 14-alpha demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,5884
Polymers103,3552
Non-polymers1,2332
Water1,49583
1
A: Lanosterol 14-alpha demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2942
Polymers51,6771
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lanosterol 14-alpha demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2942
Polymers51,6771
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.810, 55.640, 103.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Lanosterol 14-alpha demethylase / LDM / CYPLI / Cytochrome P450 51A1 / Cytochrome P450-14DM / Cytochrome P45014DM / Cytochrome P450LI ...LDM / CYPLI / Cytochrome P450 51A1 / Cytochrome P450-14DM / Cytochrome P45014DM / Cytochrome P450LI / Sterol 14-alpha demethylase


Mass: 51677.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP51A1, CYP51 / Plasmid: pCW / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: Q16850, sterol 14alpha-demethylase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 1.87 Å3/Da / Density % sol: 34 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: potassium formate, PEG 3350, n-deconyl sucrose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.73→49.01 Å / Num. obs: 22239 / % possible obs: 98.2 % / Redundancy: 4 % / Biso Wilson estimate: 54.7 Å2 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.076 / Net I/σ(I): 9.1
Reflection shellResolution: 2.73→2.8 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.874 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1597 / CC1/2: 0.672 / Rpim(I) all: 0.524 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.73→49.01 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.915 / SU B: 16.153 / SU ML: 0.319 / Cross valid method: THROUGHOUT / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24575 1101 5 %RANDOM
Rwork0.23007 ---
obs0.23085 21099 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.162 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å2-0 Å2-0 Å2
2--1.67 Å2-0 Å2
3----2.78 Å2
Refinement stepCycle: 1 / Resolution: 2.73→49.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7130 0 86 83 7299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0127444
X-RAY DIFFRACTIONr_bond_other_d0.0160.0166822
X-RAY DIFFRACTIONr_angle_refined_deg1.1051.67610112
X-RAY DIFFRACTIONr_angle_other_deg0.5831.57315906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1635888
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.144550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.965101276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0480.21078
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028408
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021536
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_it2.9965.1423558
X-RAY DIFFRACTIONr_mcbond_other2.9965.1423558
X-RAY DIFFRACTIONr_mcangle_it4.3977.7124444
X-RAY DIFFRACTIONr_mcangle_other4.3967.7134445
X-RAY DIFFRACTIONr_scbond_it4.3535.4413886
X-RAY DIFFRACTIONr_scbond_other4.3485.443884
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1188.0275668
X-RAY DIFFRACTIONr_long_range_B_refined7.0769.2988433
X-RAY DIFFRACTIONr_long_range_B_other7.07169.3048429
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.733→2.804 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 78 -
Rwork0.31 1524 -
obs--97.09 %

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