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- PDB-2pg5: Crystal Structure of Human Microsomal P450 2A6 N297Q -

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Basic information

Entry
Database: PDB / ID: 2pg5
TitleCrystal Structure of Human Microsomal P450 2A6 N297Q
ComponentsCytochrome P450 2A6
KeywordsOXIDOREDUCTASE / CYP2A6 / P450 2A6 / P450 / Monooxygenases / drug metabolizing enzyme / heme / mutant / indole
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 / CYP2E1 reactions / arachidonate epoxygenase activity / 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 / 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 / steroid metabolic process / xenobiotic catabolic process / cytoplasmic microtubule / 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 ...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: 1.95 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_conn ...database_2 / 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
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)221,45712
Polymers218,7434
Non-polymers2,7148
Water11,674648
1
A: Cytochrome P450 2A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3643
Polymers54,6861
Non-polymers6792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 2A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3643
Polymers54,6861
Non-polymers6792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P450 2A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3643
Polymers54,6861
Non-polymers6792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome P450 2A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3643
Polymers54,6861
Non-polymers6792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.853, 157.972, 103.743
Angle α, β, γ (deg.)90.000, 92.230, 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: 54685.664 Da / Num. of mol.: 4 / Mutation: 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


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 648 / 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: BL11-1 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 6, 2006
Details: flat mirror (vertical focussing) ; single crystal Si(111) bent monochromator (horizontal focussing)
RadiationMonochromator: Side scattering bent cube-root I-beam crystal; asymmetric cut 4.965 degs.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→35 Å / Num. all: 163342 / Num. obs: 163342 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Χ2: 3.194 / Net I/σ(I): 11.6
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 2.5 / Num. unique all: 15732 / Rsym value: 0.383 / Χ2: 1.183 / % possible all: 95.5

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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: 1.95→35 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 8012 4.8 %Random
Rwork0.215 ---
all0.233 155253 --
obs0.233 163265 98.7 %-
Solvent computationBsol: 39.806 Å2
Displacement parametersBiso mean: 35.387 Å2
Baniso -1Baniso -2Baniso -3
1--5.609 Å20 Å2-4.265 Å2
2---4.588 Å20 Å2
3---10.197 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.95→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15010 0 188 648 15846
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.0791.5
X-RAY DIFFRACTIONc_scbond_it2.1982
X-RAY DIFFRACTIONc_mcangle_it1.6662
X-RAY DIFFRACTIONc_scangle_it3.1962.5
LS refinement shellResolution: 1.95→2.04 Å / Rfactor Rfree error: 0.011
RfactorNum. reflection% reflection
Rfree0.322 882 -
Rwork0.292 --
obs-19195 92.8 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2xdict_heme_wat.par
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4edo.par

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