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- PDB-3gph: Human cytochrome P450 2E1 in complex with omega-imidazolyl-decano... -

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Basic information

Entry
Database: PDB / ID: 3gph
TitleHuman cytochrome P450 2E1 in complex with omega-imidazolyl-decanoic acid
ComponentsCytochrome P450 2E1
KeywordsOXIDOREDUCTASE / CYP2E1 / P450 2E1 / monooxygenase / acetaminophen / heme / fatty acid hydroxylase / Metal-binding
Function / homology
Function and homology information


: / carbon tetrachloride metabolic process / benzene metabolic process / 4-nitrophenol metabolic process / halogenated hydrocarbon metabolic process / 4-nitrophenol 2-monooxygenase activity / long-chain fatty acid omega-1 hydroxylase activity / long-chain fatty acid metabolic process / CYP2E1 reactions / arachidonate epoxygenase activity ...: / carbon tetrachloride metabolic process / benzene metabolic process / 4-nitrophenol metabolic process / halogenated hydrocarbon metabolic process / 4-nitrophenol 2-monooxygenase activity / 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 / unspecific monooxygenase / long-chain fatty acid biosynthetic process / Aspirin ADME / steroid metabolic process / Hsp70 protein binding / xenobiotic metabolic process / response to bacterium / Hsp90 protein binding / monooxygenase activity / 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 / 10-(1H-imidazol-1-yl)decanoic acid / Cytochrome P450 2E1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPorubsky, P.R. / Battaile, K.P. / Scott, E.E.
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
DepositionMar 23, 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 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Assembly

Deposited unit
A: Cytochrome P450 2E1
B: Cytochrome P450 2E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,8276
Polymers110,1172
Non-polymers1,7104
Water45025
1
A: Cytochrome P450 2E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9133
Polymers55,0581
Non-polymers8552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 2E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9133
Polymers55,0581
Non-polymers8552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.709, 70.709, 222.823
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 / P450-J


Mass: 55058.488 Da / Num. of mol.: 2 / Fragment: UNP 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, unspecific monooxygenase
#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-OID / 10-(1H-imidazol-1-yl)decanoic acid / 10-imidazolyl-decanoic acid


Mass: 238.326 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H22N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.53 Å3/Da / Density % sol: 51.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Na HEPES, 5% Isopropanol, 20% PEG 2000 MME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 2, 2008
Details: Sagitally focused second crystal, vertical focusing via a one-meter, Pt/Pd-coated cylindrically focusing mirror
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 28495 / Num. obs: 28493 / % possible obs: 95.4 % / Redundancy: 6.7 % / Biso Wilson estimate: 51.075 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 17.071
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.457 / Num. unique all: 2034 / % possible all: 93.4

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Processing

Software
NameVersionClassification
MAR345CCDdata collection
PHASERphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3E61

3e61


Resolution: 2.7→31.31 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.86 / SU B: 14.75 / SU ML: 0.301 / Cross valid method: THROUGHOUT / ESU R Free: 0.42
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28261 1442 5.1 %RANDOM
Rwork0.21245 ---
obs0.21609 27040 95.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.748 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.7→31.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7530 0 120 25 7675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0227881
X-RAY DIFFRACTIONr_angle_refined_deg1.9092.01110694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5175920
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.53723.164373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.783151345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.0481558
X-RAY DIFFRACTIONr_chiral_restr0.1360.21129
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026044
X-RAY DIFFRACTIONr_nbd_refined0.2360.23654
X-RAY DIFFRACTIONr_nbtor_refined0.3150.25117
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2218
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.246
X-RAY DIFFRACTIONr_mcbond_it0.6771.54812
X-RAY DIFFRACTIONr_mcangle_it1.17227538
X-RAY DIFFRACTIONr_scbond_it1.82833501
X-RAY DIFFRACTIONr_scangle_it2.7974.53151
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 97 -
Rwork0.266 1937 -
obs--93.47 %

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