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- PDB-3mdv: Clotrimazole complex of Cytochrome P450 46A1 -

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Basic information

Entry
Database: PDB / ID: 3mdv
TitleClotrimazole complex of Cytochrome P450 46A1
ComponentsCholesterol 24-hydroxylase
KeywordsOXIDOREDUCTASE / CYP46A1 / P450 46A1 / P450 / CLOTRIMAZOLE / MONOOXYGENASE / METABOLIC ENZYME / HEME / Cholesterol metabolism / Endoplasmic reticulum / Iron / Lipid metabolism / Membrane / Metal-binding / Microsome / NADP / Steroid metabolism / Transmembrane
Function / homology
Function and homology information


cholesterol 24-hydroxylase / cholesterol 24-hydroxylase activity / protein localization to membrane raft / testosterone 16-beta-hydroxylase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / progesterone metabolic process / sterol metabolic process / bile acid biosynthetic process / regulation of long-term synaptic potentiation / steroid hydroxylase activity ...cholesterol 24-hydroxylase / cholesterol 24-hydroxylase activity / protein localization to membrane raft / testosterone 16-beta-hydroxylase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / progesterone metabolic process / sterol metabolic process / bile acid biosynthetic process / regulation of long-term synaptic potentiation / steroid hydroxylase activity / Endogenous sterols / cholesterol catabolic process / xenobiotic metabolic process / presynapse / nervous system development / postsynapse / iron ion binding / dendrite / heme binding / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Cholesterol 24-hydroxylase / Cytochrome P450, E-class, group I / 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
1-[(2-CHLOROPHENYL)(DIPHENYL)METHYL]-1H-IMIDAZOLE / PROTOPORPHYRIN IX CONTAINING FE / Cholesterol 24-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMast, N. / Charvet, C. / Pikuleva, I. / Stout, C.D.
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: Structural basis of drug binding to CYP46A1, an enzyme that controls cholesterol turnover in the brain.
Authors: Mast, N. / Charvet, C. / Pikuleva, I.A. / Stout, C.D.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Crystal structures of substrate-bound and substrate-free cytochrome P450 46A1, the principal cholesterol hydroxylase in the brain.
Authors: Mast, N. / White, M.A. / Bjorkhem, I. / Johnson, E.F. / Stout, C.D. / Pikuleva, I.A.
History
DepositionMar 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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: Cholesterol 24-hydroxylase
B: Cholesterol 24-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,1736
Polymers104,2502
Non-polymers1,9234
Water8,719484
1
A: Cholesterol 24-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0863
Polymers52,1251
Non-polymers9612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cholesterol 24-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0863
Polymers52,1251
Non-polymers9612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.610, 121.610, 144.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-957-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 3 / Auth seq-ID: 59 - 489 / Label seq-ID: 11 - 441

Dom-IDAuth asym-IDLabel asym-ID
1BB
2AA

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Components

#1: Protein Cholesterol 24-hydroxylase / CH24H / Cytochrome P450 46A1


Mass: 52125.086 Da / Num. of mol.: 2 / Fragment: UNP residues 51-500
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP46A1, CYP46 / Plasmid: PUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: Q9Y6A2, EC: 1.14.13.98
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CL6 / 1-[(2-CHLOROPHENYL)(DIPHENYL)METHYL]-1H-IMIDAZOLE / CLOTRIMAZOLE


Mass: 344.837 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H17ClN2 / Comment: medication, antifungal*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.6 Å3/Da / Density % sol: 52.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 14% PEG 8000, 20% glycerol, 50 mM KPi, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 31, 2009 / Details: Rh coated flat mirror
RadiationMonochromator: side scattering I-beam bent single crystal, asymmetric cut 4.9650 deg
Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.459
11-H, K, -L20.541
ReflectionResolution: 2.4→93.074 Å / Num. all: 39099 / Num. obs: 39099 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 42.7 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 4.6
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 1.9 / Num. unique all: 5847 / Rsym value: 0.396 / % possible all: 97.2

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q9F

2q9f


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.909 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.573 / SU ML: 0.153 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY TWIN DOMAINS: H,K,L TWIN FRACTION 0.459 -H,K,-L TWIN FRACTION 0.541
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1909 5 %RANDOM
Rwork0.209 ---
all0.21 38134 --
obs0.21 36225 92.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 71.73 Å2 / Biso mean: 32.556 Å2 / Biso min: 2.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6836 0 136 484 7456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0217968
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.96112204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5657.51688
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.65523.193332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.601151284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3471568
X-RAY DIFFRACTIONr_chiral_restr0.0960.21046
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218846
X-RAY DIFFRACTIONr_mcbond_it0.6571.54226
X-RAY DIFFRACTIONr_mcangle_it1.26426830
X-RAY DIFFRACTIONr_scbond_it1.9232898
X-RAY DIFFRACTIONr_scangle_it3.2174.52802
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1696TIGHT POSITIONAL0.030.05
1722LOOSE POSITIONAL0.075
1696TIGHT THERMAL0.070.5
1722LOOSE THERMAL0.0810
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.19 114 -
Rwork0.169 1848 -
all-1962 -
obs-1848 65.2 %

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