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- PDB-3koh: Cytochrome P450 2E1 with omega-imidazolyl octanoic acid -

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Basic information

Entry
Database: PDB / ID: 3koh
TitleCytochrome P450 2E1 with omega-imidazolyl octanoic acid
ComponentsCytochrome P450 2E1
KeywordsOXIDOREDUCTASE / CYP2E1 / P450 2E1 / monooxygenase / heme / fatty acid / microsome / membrane / Endoplasmic reticulum / Iron / Metal-binding
Function / homology
Function and homology information


: / 4-nitrophenol 2-monooxygenase activity / carbon tetrachloride metabolic process / benzene metabolic process / 4-nitrophenol metabolic process / halogenated hydrocarbon metabolic process / long-chain fatty acid omega-1 hydroxylase activity / long-chain fatty acid metabolic process / CYP2E1 reactions / arachidonate epoxygenase activity ...: / 4-nitrophenol 2-monooxygenase activity / carbon tetrachloride metabolic process / benzene metabolic process / 4-nitrophenol metabolic process / halogenated hydrocarbon metabolic process / long-chain fatty acid omega-1 hydroxylase activity / long-chain fatty acid metabolic process / CYP2E1 reactions / arachidonate epoxygenase activity / epoxygenase P450 pathway / lipid hydroxylation / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / Biosynthesis of maresin-like SPMs / monoterpenoid metabolic process / Xenobiotics / Paracetamol ADME / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / long-chain fatty acid biosynthetic process / unspecific monooxygenase / aromatase activity / Aspirin ADME / steroid metabolic process / Hsp70 protein binding / xenobiotic metabolic process / monooxygenase activity / response to bacterium / Hsp90 protein binding / oxygen binding / mitochondrial inner membrane / oxidoreductase activity / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / enzyme binding / cytoplasm
Similarity search - Function
Cytochrome P450, E-class, group I, CYP2E-like / : / 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 ...Cytochrome P450, E-class, group I, CYP2E-like / : / 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
PROTOPORPHYRIN IX CONTAINING FE / 8-(1H-imidazol-1-yl)octanoic acid / Cytochrome P450 2E1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsScott, E.E. / Porubsky, P.R.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Human cytochrome P450 2E1 structures with fatty acid analogs reveal a previously unobserved binding mode.
Authors: Porubsky, P.R. / Battaile, K.P. / Scott, E.E.
History
DepositionNov 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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: Cytochrome P450 2E1
B: Cytochrome P450 2E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,7706
Polymers110,1172
Non-polymers1,6544
Water19811
1
A: Cytochrome P450 2E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8853
Polymers55,0581
Non-polymers8272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 2E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8853
Polymers55,0581
Non-polymers8272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.185, 71.185, 224.862
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Cytochrome P450 2E1 / CYPIIE1 / 4-nitrophenol 2-hydroxylase / P450-J


Mass: 55058.488 Da / Num. of mol.: 2 / Fragment: UNP residues 31-493
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP2E, CYP2E1 / Plasmid: pKK2E1dH / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP3
References: UniProt: P05181, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor
#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-OIO / 8-(1H-imidazol-1-yl)octanoic acid


Mass: 210.273 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Na HEPES pH 7.5, 5% Isopropanol, 22% PEG 2000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 21, 2009 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→38.01 Å / Num. obs: 24282 / % possible obs: 98.3 % / Redundancy: 4.2 % / Rsym value: 0.123
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.436 / % possible all: 99.1

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Processing

Software
NameVersionClassification
Blu-IceICEdata collection
PHASERphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3E6I

3e6i


Resolution: 2.9→35.59 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.852 / SU B: 21.131 / SU ML: 0.396 / Cross valid method: THROUGHOUT / ESU R Free: 0.501 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29199 1217 5 %RANDOM
Rwork0.20647 ---
obs0.2107 23000 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.771 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å2-0 Å2
2--0.06 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.9→35.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7554 0 116 11 7681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227894
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5272.01110712
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6265924
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64923.172372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.989151350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3281558
X-RAY DIFFRACTIONr_chiral_restr0.1030.21130
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216058
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5531.54644
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.08327564
X-RAY DIFFRACTIONr_scbond_it1.47233250
X-RAY DIFFRACTIONr_scangle_it2.5864.53148
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 78 -
Rwork0.255 1693 -
obs--96.41 %

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