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- PDB-2pg6: Crystal Structure of Human Microsomal P450 2A6 L240C/N297Q -

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Basic information

Entry
Database: PDB / ID: 2pg6
TitleCrystal Structure of Human Microsomal P450 2A6 L240C/N297Q
ComponentsCytochrome P450 2A6
KeywordsOXIDOREDUCTASE / CYP2A6 / P450 2A6 / P450 / Monooxygenases / drug metabolizing enzyme / heme / indole / mutant
Function / homology
Function and homology information


coumarin catabolic process / coumarin 7-hydroxylase activity / Fatty acids / coumarin metabolic process / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor / arachidonic acid epoxygenase activity / CYP2E1 reactions / epoxygenase P450 pathway / aflatoxin metabolic process / Aflatoxin activation and detoxification ...coumarin catabolic process / coumarin 7-hydroxylase activity / Fatty acids / coumarin metabolic process / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor / arachidonic acid epoxygenase activity / CYP2E1 reactions / 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 / aromatase activity / cytoplasmic microtubule / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / monooxygenase 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, 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
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 2A6 / Cytochrome P450 2A13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsSansen, S. / Hsu, M.H. / Stout, C.D. / Johnson, E.F.
CitationJournal: Arch.Biochem.Biophys. / Year: 2007
Title: Structural insight into the altered substrate specificity of human cytochrome P450 2A6 mutants.
Authors: Sansen, S. / Hsu, M.H. / Stout, C.D. / Johnson, E.F.
History
DepositionApr 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 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
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450 2A6
B: Cytochrome P450 2A6
C: Cytochrome P450 2A6
D: Cytochrome P450 2A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,1698
Polymers218,7034
Non-polymers2,4664
Water5,567309
1
A: Cytochrome P450 2A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2922
Polymers54,6761
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 2A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2922
Polymers54,6761
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P450 2A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2922
Polymers54,6761
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome P450 2A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2922
Polymers54,6761
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.700, 158.245, 103.764
Angle α, β, γ (deg.)90.000, 92.090, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly has not been determined but thought to be a monomer

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Components

#1: Protein
Cytochrome P450 2A6 / CYPIIA6 / Coumarin 7-hydroxylase / P450 IIA3 / CYP2A3 / P450I


Mass: 54675.648 Da / Num. of mol.: 4 / Mutation: L240C, N297Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP2A6 / Plasmid: PCWORI / Production host: Escherichia coli (E. coli) / Strain (production host): DC5
References: UniProt: P11509, UniProt: Q16696*PLUS, unspecific monooxygenase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.65 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG3350, Tris, ammonium sulfate, Anapoe-35, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 27, 2005
Details: Double-crystal monochromator, 1m long Rh coated bent cylindrical mirror for horizontal and vertical focussing
RadiationMonochromator: Double crystal, parallel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.53→50 Å / Num. all: 70956 / Num. obs: 70956 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Χ2: 2.123 / Net I/σ(I): 8.7
Reflection shellResolution: 2.53→2.59 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 3.4 / Num. unique all: 6642 / Rsym value: 0.238 / Χ2: 0.77 / % possible all: 88.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
Blu-Icedata collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: coumarin complex of CYP2A6, PDB entry 1Z10

1z10


Resolution: 2.53→40 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 3604 4.6 %random
Rwork0.209 ---
all0.239 67294 --
obs0.239 70898 90.1 %-
Solvent computationBsol: 23.375 Å2
Displacement parametersBiso mean: 34.145 Å2
Baniso -1Baniso -2Baniso -3
1--8.544 Å20 Å2-2.663 Å2
2---3.689 Å20 Å2
3---12.233 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.53→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15015 0 172 315 15502
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.0351.5
X-RAY DIFFRACTIONc_scbond_it1.6322
X-RAY DIFFRACTIONc_mcangle_it1.6712
X-RAY DIFFRACTIONc_scangle_it2.3942.5
LS refinement shellResolution: 2.53→2.64 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection% reflection
Rfree0.339 419 -
Rwork0.27 --
obs-7690 81 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:xdict_heme.par
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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