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- PDB-2q9f: Crystal structure of human cytochrome P450 46A1 in complex with c... -

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Basic information

Entry
Database: PDB / ID: 2q9f
TitleCrystal structure of human cytochrome P450 46A1 in complex with cholesterol-3-sulphate
ComponentsCytochrome P450 46A1
KeywordsOXIDOREDUCTASE / CYP46A1 / P450 46A1 / P450 / MONOOXYGENASE / CHOLESTEROL METABOLIC ENZYME / HEME / cholesterol-3-sulphate
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
CHOLEST-5-EN-3-YL HYDROGEN SULFATE / PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / Cholesterol 24-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.9 Å
AuthorsWhite, M.A. / Mast, N.V. / Johnson, E.F. / Stout, C.D. / Pikuleva, I.A.
Citation
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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Use of complementary cation and anion heavy-atom salt derivatives to solve the structure of cytochrome P450 46A1.
Authors: White, M.A. / Mast, N. / Bjorkhem, I. / Johnson, E.F. / Stout, C.D. / Pikuleva, I.A.
History
DepositionJun 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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 46A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,85610
Polymers52,1251
Non-polymers1,7319
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.850, 121.850, 144.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 52125.086 Da / Num. of mol.: 1 / Fragment: 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

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Non-polymers , 5 types, 139 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-C3S / CHOLEST-5-EN-3-YL HYDROGEN SULFATE / CHOLESTEROL-SULFATE


Mass: 466.717 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O4S
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.4 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: PEG8000, Potassium Phosphate, Glycerol, NaCl, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K, pH 4.6, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 30, 2007
Details: FLAT MIRROR (VERTICAL FOCUSING), SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HO RIZONTAL FOCUSING)
RadiationMonochromator: SIDE SCATTERING BENT CUBE- ROOT I-BEAM SINGLE CRYSTAL, ASYMMETRIC CUT 4.965 DEGS
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.9→44.68 Å / Num. all: 42756 / Num. obs: 42756 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 32.5 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 14.8
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.97 / % possible all: 100

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1.1refinement
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 1.9→43.08 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 4155867.19 / Data cutoff low absF: 0 / Isotropic thermal model: variable / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Refmac5 and TLS used in intermediate refinement steps. TLS not used in CNS refinement. TLS groups determined using the TLSMD server. TLSMD REF: J Painter & E A Merritt (2006) J. Appl. Cryst. ...Details: Refmac5 and TLS used in intermediate refinement steps. TLS not used in CNS refinement. TLS groups determined using the TLSMD server. TLSMD REF: J Painter & E A Merritt (2006) J. Appl. Cryst. 39, 109-111. PMB used in all CNS refinements: PMB BOND target set to 0.020, PMB Variable Sigma-B used default parameters. PMB Hydrogen bond restraints not used. PMB Local scale reject set to 30 sigma, PMB Local Scale rejected 213 reflections of 42738, PMB Local Scale rejected reflections test flag+=90. PMB Local Scale (h,k,l) box sizes = +/- 4 3 5, PMB Local Scale maximum scale used (localscale method): 15.179, PMB Local Scale minimum scale used (localscale method): 6.502
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2025 4.9 %THICK SHELLS
Rwork0.183 ---
all0.18727 40957 --
obs0.183 40957 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.8114 Å2 / ksol: 0.360044 e/Å3
Displacement parametersBiso mean: 45.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.9→43.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3488 0 116 130 3734
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d6.58
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.9→1.93 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 114 6.3 %
Rwork0.288 1684 -
obs-1798 85.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep_pmb.paramprotein_pmb.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4ligand.paramligand.top
X-RAY DIFFRACTION5carbohydrate.param

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