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- PDB-2hi4: Crystal Structure of Human Microsomal P450 1A2 in complex with al... -

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Basic information

Entry
Database: PDB / ID: 2hi4
TitleCrystal Structure of Human Microsomal P450 1A2 in complex with alpha-naphthoflavone
ComponentsCytochrome P450 1A2
KeywordsOXIDOREDUCTASE / CYP1A2 / P450 1A2 / P450 / monooxygenase / drug metabolizing enzyme / alpha-naphthoflavone / Benzo(h)flavone / 7 / 8-Benzoflavone / heme
Function / homology
Function and homology information


xenobiotic catabolic process => GO:0042178 / : / Aromatic amines can be N-hydroxylated or N-dealkylated by CYP1A2 / xenobiotic catabolic process => GO:0042178 / dibenzo-p-dioxin metabolic process / xenobiotic metabolic process => GO:0006805 / hydroperoxy icosatetraenoate dehydratase / hydroperoxy icosatetraenoate dehydratase activity / monocarboxylic acid metabolic process / toxin biosynthetic process ...xenobiotic catabolic process => GO:0042178 / : / Aromatic amines can be N-hydroxylated or N-dealkylated by CYP1A2 / xenobiotic catabolic process => GO:0042178 / dibenzo-p-dioxin metabolic process / xenobiotic metabolic process => GO:0006805 / hydroperoxy icosatetraenoate dehydratase / hydroperoxy icosatetraenoate dehydratase activity / monocarboxylic acid metabolic process / toxin biosynthetic process / Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE) / omega-hydroxylase P450 pathway / porphyrin-containing compound metabolic process / epoxygenase P450 pathway / Biosynthesis of protectins / caffeine oxidase activity / estrogen 16-alpha-hydroxylase activity / estrogen 2-hydroxylase activity / : / alkaloid metabolic process / demethylase activity / Aflatoxin activation and detoxification / Biosynthesis of maresin-like SPMs / Methylation / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / monoterpenoid metabolic process / : / oxidative demethylation / steroid catabolic process / 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 / hydrogen peroxide biosynthetic process / long-chain fatty acid biosynthetic process / cellular respiration / estrogen metabolic process / retinol metabolic process / unspecific monooxygenase / aromatase activity / response to immobilization stress / cellular response to copper ion / cellular response to cadmium ion / xenobiotic metabolic process / cholesterol metabolic process / post-embryonic development / monooxygenase activity / lung development / response to estradiol / methylation / regulation of gene expression / response to lipopolysaccharide / electron transfer activity / oxidoreductase activity / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / enzyme binding
Similarity search - Function
Cytochrome P450, E-class, group I, CYP1 / 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
2-PHENYL-4H-BENZO[H]CHROMEN-4-ONE / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 1A2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSansen, S. / Yano, J.K. / Reynald, R.L. / Schoch, G.S. / Stout, C.D. / Johnson, E.F.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Adaptations for the oxidation of polycyclic aromatic hydrocarbons exhibited by the structure of human P450 1A2.
Authors: Sansen, S. / Yano, J.K. / Reynald, R.L. / Schoch, G.A. / Griffin, K.J. / Stout, C.D. / Johnson, E.F.
History
DepositionJun 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Aug 30, 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.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_conn.ptnr2_label_seq_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 1A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1823
Polymers56,2941
Non-polymers8892
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.630, 80.820, 175.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
DetailsThe biological assembly has not been determined but thought to be a monomer

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Components

#1: Protein Cytochrome P450 1A2 / CYPIA2 / P450-P3 / P3 / 450 / P450 4


Mass: 56293.582 Da / Num. of mol.: 1 / Fragment: Residues 26-514
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP1A2 / Plasmid: pCWori / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P05177, unspecific monooxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-BHF / 2-PHENYL-4H-BENZO[H]CHROMEN-4-ONE / 7,8-BENZOFLAVONE / ALPHA-NAPHTHOFLAVONE / Alpha-Naphthoflavone


Mass: 272.297 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H12O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG3350, Tris, ammonium nitrate, Cymal-6 (cyclohexyl-hexyl-beta-D-maltoside), C12E8 (octaethyleneglycol mono-n-dodecyl ether) , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2006
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→88.045 Å / Num. all: 41139 / Num. obs: 41139 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 23.73 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 4
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 1.5 / Num. measured all: 15186 / Num. unique all: 3092 / Rsym value: 0.394 / % possible all: 95.2

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CYP2A6, PDB entry 1Z10

1z10


Resolution: 1.95→29.51 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2726889.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1871 4.9 %RANDOM
Rwork0.226 ---
obs0.223 38022 91.1 %-
all-39893 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.449 Å2 / ksol: 0.424 e/Å3
Displacement parametersBiso mean: 37.6 Å2
Baniso -1Baniso -2Baniso -3
1-24.99 Å20 Å20 Å2
2---12.86 Å20 Å2
3----12.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 1.95→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3844 0 64 160 4068
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d1.26
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.383 325 5 %
Rwork0.371 6145 -
obs-6470 94.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3xdict_heme_relax.parxdict_heme.top
X-RAY DIFFRACTION4bhf.parbhf.top

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