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- PDB-3lc4: Human Cytochrome P450 2E1 in Complex with Omega-Imidazolyl-Dodeca... -

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Basic information

Entry
Database: PDB / ID: 3lc4
TitleHuman Cytochrome P450 2E1 in Complex with Omega-Imidazolyl-Dodecanoic Acid
ComponentsCytochrome P450 2E1
KeywordsOXIDOREDUCTASE / CYP2E1 / P450 2E1 / monooxygenase / acetaminophen / heme / endoplasmic reticulum / iron / membrane / metal-binding / microsome
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 / CYP2E1 reactions / long-chain fatty acid metabolic process / 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 / CYP2E1 reactions / long-chain fatty acid metabolic process / 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 / long-chain fatty acid biosynthetic process / unspecific monooxygenase / 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 / Aspirin ADME / steroid metabolic process / Hsp70 protein binding / xenobiotic metabolic process / monooxygenase activity / response to bacterium / Hsp90 protein binding / oxygen binding / oxidoreductase activity / mitochondrial inner membrane / 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 / 12-(1H-imidazol-1-yl)dodecanoic acid / Cytochrome P450 2E1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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
DepositionJan 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 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_asym_id / _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.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_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_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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)111,8836
Polymers110,1172
Non-polymers1,7664
Water905
1
A: Cytochrome P450 2E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9413
Polymers55,0581
Non-polymers8832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 2E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9413
Polymers55,0581
Non-polymers8832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.779, 70.779, 224.629
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: sequence database residues 32-493
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-LC4 / 12-(1H-imidazol-1-yl)dodecanoic acid


Mass: 266.379 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H26N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.55 Å3/Da / Density % sol: 51.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: NaHEPES pH 7.5, 5% iso-propanol, 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: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 1, 2009 / Details: mirrors
RadiationMonochromator: SIDE-SCATTERING CUBEROOT I- BEAM BENT SINGLE CRYSTAL. ASYMMETRIC CUT 12.2 DEGS
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.1→38.01 Å / Num. obs: 19925 / % possible obs: 100 % / Redundancy: 12.3 % / Rsym value: 0.189
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 1443 / Rsym value: 0.405 / % possible all: 100

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Processing

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

3e6i


Resolution: 3.1→37.93 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.848 / SU B: 24.186 / SU ML: 0.429 / Cross valid method: THROUGHOUT / ESU R Free: 0.543 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27013 1018 5.1 %RANDOM
Rwork0.1977 ---
obs0.20139 18847 99.79 %-
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: 47.046 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å2-0 Å2
2---0.14 Å2-0 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 3.1→37.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7502 0 124 5 7631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227848
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5042.01210648
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3455915
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61723.135370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.341151335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7751558
X-RAY DIFFRACTIONr_chiral_restr0.0980.21125
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216014
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_it0.4981.54609
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.97527508
X-RAY DIFFRACTIONr_scbond_it1.3533239
X-RAY DIFFRACTIONr_scangle_it2.4214.53140
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.103→3.183 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 76 -
Rwork0.247 1313 -
obs--97.41 %

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