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- PDB-3dax: Crystal structure of human CYP7A1 -

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Basic information

Entry
Database: PDB / ID: 3dax
TitleCrystal structure of human CYP7A1
ComponentsCytochrome P450 7A1
KeywordsOXIDOREDUCTASE / cytochrome p450 / cholesterol / cholesterol 7-alpha hydroxylase / Structural Genomics / Structural Genomics Consortium / SGC / Cholesterol metabolism / Endoplasmic reticulum / Heme / Iron / Lipid metabolism / Membrane / Metal-binding / Microsome / Monooxygenase / NADP / Polymorphism / Steroid metabolism
Function / homology
Function and homology information


cholesterol 7alpha-monooxygenase / 24-hydroxycholesterol 7alpha-hydroxylase / cholesterol 7-alpha-monooxygenase activity / 24-hydroxycholesterol 7alpha-hydroxylase activity / negative regulation of collagen biosynthetic process / cellular response to cholesterol / sterol metabolic process / negative regulation of fatty acid biosynthetic process / regulation of bile acid biosynthetic process / positive regulation of cholesterol biosynthetic process ...cholesterol 7alpha-monooxygenase / 24-hydroxycholesterol 7alpha-hydroxylase / cholesterol 7-alpha-monooxygenase activity / 24-hydroxycholesterol 7alpha-hydroxylase activity / negative regulation of collagen biosynthetic process / cellular response to cholesterol / sterol metabolic process / negative regulation of fatty acid biosynthetic process / regulation of bile acid biosynthetic process / positive regulation of cholesterol biosynthetic process / bile acid biosynthetic process / bile acid and bile salt transport / bile acid signaling pathway / Synthesis of bile acids and bile salts / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / cholesterol catabolic process / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / cholesterol homeostasis / cellular response to glucose stimulus / PPARA activates gene expression / response to ethanol / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane
Similarity search - Function
Cholesterol 7-alpha-monooxygenase / Cytochrome P450, cholesterol 7-alpha-monooxygenase-type / Cytochrome P450, E-class, group IV / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 ...Cholesterol 7-alpha-monooxygenase / Cytochrome P450, cholesterol 7-alpha-monooxygenase-type / Cytochrome P450, E-class, group IV / 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
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 7A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement, molecular replacement / molecular replacement / Resolution: 2.15 Å
AuthorsStrushkevich, N.V. / Tempel, W. / Dombrovski, L. / Dong, A. / Loppnau, P. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Wilkstrom, M. / Bochkarev, A. ...Strushkevich, N.V. / Tempel, W. / Dombrovski, L. / Dong, A. / Loppnau, P. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Wilkstrom, M. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human CYP7A1
Authors: Strushkevich, N.V. / Tempel, W. / Dombrovski, L. / Dong, A. / Loppnau, P. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Wilkstrom, M. / Bochkarev, A. / Park, H.
History
DepositionMay 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 21, 2020Group: Data collection / Derived calculations / Category: phasing / struct_site
Item: _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 7A1
B: Cytochrome P450 7A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,1736
Polymers112,9402
Non-polymers1,2334
Water2,342130
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-22 kcal/mol
Surface area38870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.339, 80.159, 84.937
Angle α, β, γ (deg.)64.360, 75.230, 72.170
Int Tables number1
Space group name H-MP1
DetailsAuthors state that the biological assembly is not known.

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Components

#1: Protein Cytochrome P450 7A1 / Cholesterol 7-alpha-monooxygenase / CYPVII / Cholesterol 7-alpha-hydroxylase


Mass: 56469.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP7A1, CYP7 / Plasmid: pCW / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P22680, EC: 1.14.13.17
#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-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#4: 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
1358.3
2358.3
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.5
Details: 20% PEG400, 0.1M potassium chloride, 0.1M trisodium citrate, pH 5.5, vapor diffusion, temperature 291K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2510.9686
2
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 21, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 65596 / % possible obs: 92 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.063 / Χ2: 1.179 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.1-2.183.10.40248180.97868.2
2.18-2.263.30.31456381.02378.7
2.26-2.373.40.27662731.01287.8
2.37-2.493.60.2568391.06295.2
2.49-2.653.80.19469481.04697.6
2.65-2.853.90.14569891.07498
2.85-3.143.90.08969891.12398.3
3.14-3.593.90.05370251.21598.5
3.59-4.523.90.03570601.44698.7
4.52-403.80.02970171.6198.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.3.0037refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
MolProbitymodel building
RefinementMethod to determine structure: molecular replacement, molecular replacement
Starting model: pdb entry 2iag

2iag


Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.179 / SU B: 5.221 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.213 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2018 3.201 %thin shells (sftools)
Rwork0.189 ---
obs0.19 63038 93.449 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.625 Å2
Baniso -1Baniso -2Baniso -3
1--0.061 Å2-0.162 Å2-0.007 Å2
2--0.081 Å20.19 Å2
3----0.081 Å2
Refinement stepCycle: LAST / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7519 0 88 130 7737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0227817
X-RAY DIFFRACTIONr_bond_other_d0.0020.025284
X-RAY DIFFRACTIONr_angle_refined_deg1.2881.99310633
X-RAY DIFFRACTIONr_angle_other_deg0.877312872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9695964
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13123.704351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.595151314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1851542
X-RAY DIFFRACTIONr_chiral_restr0.0790.21156
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028671
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021619
X-RAY DIFFRACTIONr_nbd_refined0.2020.21571
X-RAY DIFFRACTIONr_nbd_other0.1880.25138
X-RAY DIFFRACTIONr_nbtor_refined0.1780.23776
X-RAY DIFFRACTIONr_nbtor_other0.0860.23968
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2215
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0980.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2050.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.26
X-RAY DIFFRACTIONr_mcbond_it2.52624951
X-RAY DIFFRACTIONr_mcbond_other0.61521901
X-RAY DIFFRACTIONr_mcangle_it3.60637628
X-RAY DIFFRACTIONr_scbond_it2.43223364
X-RAY DIFFRACTIONr_scangle_it3.39332988
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.20600.253645502272.581
2.206-2.26600.2273804478779.465
2.266-2.3310.283970.2363673472686.119
2.331-2.40200.2264214462491.133
2.402-2.480.2953630.2273813438195.321
2.48-2.56700.2194194430897.354
2.567-2.66300.2134050414497.732
2.663-2.7710.2992900.2143655402398.061
2.771-2.89300.2093701377298.118
2.893-3.0330.2622750.2013319366498.09
3.033-3.19500.1923425347798.504
3.195-3.3860.222260.1873031330898.458
3.386-3.61700.1733013306098.464
3.617-3.9020.1891590.1652703289798.792
3.902-4.26700.1512638267698.58
4.267-4.7590.1531240.1452217237398.651
4.759-5.4720.183860.162011215297.444
5.472-6.6470.284480.2061743181098.95
6.647-9.1780.219230.1851393142099.718
9.178-300.175270.20277883396.639

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