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- PDB-4eji: Human Cytochrome P450 2A13 in complex with two molecules of 4-(me... -

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Basic information

Entry
Database: PDB / ID: 4eji
TitleHuman Cytochrome P450 2A13 in complex with two molecules of 4-(methylnitrosamino)-1-(3-puridyl)-1-butanone
ComponentsCytochrome P450 2A13
KeywordsOXIDOREDUCTASE / CYP2A13 / cytochrome P450 2A13 / P450 2A13 / heme protein / monooxygenase / drug metabolism / xenobiotic metabolism / endoplasmic reticulum / membrane
Function / homology
Function and homology information


coumarin 7-hydroxylase activity / Fatty acids / coumarin metabolic process / CYP2E1 reactions / arachidonate epoxygenase activity / epoxygenase P450 pathway / aflatoxin metabolic process / Aflatoxin activation and detoxification / Xenobiotics / 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 ...coumarin 7-hydroxylase activity / Fatty acids / coumarin metabolic process / CYP2E1 reactions / arachidonate epoxygenase activity / epoxygenase P450 pathway / aflatoxin metabolic process / Aflatoxin activation and detoxification / Xenobiotics / 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 / xenobiotic metabolic process / monooxygenase activity / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / cytoplasm
Similarity search - Function
Cytochrome P450, E-class, group I, CYP2A-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, CYP2A-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
Chem-0QA / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 2A13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDeVore, N.M. / Scott, E.E.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Nicotine and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone binding and access channel in human cytochrome P450 2A6 and 2A13 enzymes.
Authors: DeVore, N.M. / Scott, E.E.
History
DepositionApr 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 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_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_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 2A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8364
Polymers54,8051
Non-polymers1,0313
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.807, 122.807, 194.213
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Cytochrome P450 2A13 / CYPIIA13


Mass: 54804.758 Da / Num. of mol.: 1 / Fragment: unp residues 31-494
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP2A13 / Plasmid: pKK2A13dH / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP3 / References: UniProt: Q16696, unspecific monooxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-0QA / 4-[methyl(nitroso)amino]-1-(pyridin-3-yl)butan-1-one


Mass: 207.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 3.34 Å3/Da / Density % sol: 63.18 %
Crystal growTemperature: 298 K / pH: 7.8
Details: 4.0 M sodium formate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 27, 2012 / Details: RH COAT FLAT MIRROR, TOROIDAL FOCUSING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→97.11 Å / Num. obs: 43580 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 14.7 % / Biso Wilson estimate: 41.1 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.104 / Net I/σ(I): 18.3
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 14.8 % / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERMRphasing
REFMAC6.1.13refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P85

2p85


Resolution: 2.1→51.9 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.629 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.155
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2191 5 %RANDOM
Rwork0.201 ---
obs0.203 41386 100 %-
all-41386 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.98 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.1→51.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3763 0 73 69 3905
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 166 -
Rwork0.284 3008 -
obs--100 %

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