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- PDB-3mdm: Thioperamide complex of Cytochrome P450 46A1 -

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Basic information

Entry
Database: PDB / ID: 3mdm
TitleThioperamide complex of Cytochrome P450 46A1
ComponentsCholesterol 24-hydroxylase
KeywordsOXIDOREDUCTASE / CYP46A1 / P450 46A1 / P450 / THIOPERAMIDE / 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 / bile acid biosynthetic process / progesterone metabolic process / testosterone 6-beta-hydroxylase activity / sterol metabolic process / 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 / bile acid biosynthetic process / progesterone metabolic process / testosterone 6-beta-hydroxylase activity / sterol metabolic process / steroid hydroxylase activity / cholesterol catabolic process / regulation of long-term synaptic potentiation / Endogenous sterols / xenobiotic metabolic process / nervous system development / presynapse / postsynapse / iron ion binding / heme binding / dendrite / 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
Chem-FJZ / PROTOPORPHYRIN IX CONTAINING FE / Cholesterol 24-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 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_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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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: Cholesterol 24-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0343
Polymers52,1251
Non-polymers9092
Water13,944774
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.830, 85.820, 104.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 52125.086 Da / Num. of mol.: 1 / Fragment: UNP residues 51-500
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP46, CYP46A1 / 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.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-FJZ / N-cyclohexyl-4-(1H-imidazol-5-yl)piperidine-1-carbothioamide


Mass: 292.443 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 774 / 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: 2.56 Å3/Da / Density % sol: 51.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 8% PEG 8000, 20% glycerol, 50 mM KPi, pH 5.8, 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 10, 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
ReflectionResolution: 1.6→66.242 Å / Num. all: 70320 / Num. obs: 70320 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 3.7
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 1.6 / Num. unique all: 10140 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q9F

2q9f


Resolution: 1.6→20 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 3505 5 %RANDOM
Rwork0.182 ---
all0.182 69649 --
obs0.182 69649 99.2 %-
Solvent computationBsol: 43.544 Å2
Displacement parametersBiso max: 55.61 Å2 / Biso mean: 22.297 Å2 / Biso min: 6.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.296 Å20 Å20 Å2
2--0.366 Å20 Å2
3----0.662 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3503 0 63 774 4340
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0191.5
X-RAY DIFFRACTIONc_angle_deg1.862
X-RAY DIFFRACTIONc_dihedral_angle_d5.5842
X-RAY DIFFRACTIONc_improper_angle_d0.0082.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2heme_Hic-up.par
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4thioperamide_092509.par

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