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- PDB-4ejg: Human Cytochrome P450 2A13 in complex with Nicotine -

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Basic information

Entry
Database: PDB / ID: 4ejg
TitleHuman Cytochrome P450 2A13 in complex with Nicotine
ComponentsCytochrome P450 2A13
KeywordsOXIDOREDUCTASE / CYP2A13 / cytochrome P450 2A13 / heme protein / P450 2A13 / monooxygenase / drug metabolism / xenobiotic metabolism / endoplasmic reticulum / membrane
Function / homology
Function and homology information


coumarin 7-hydroxylase activity / Fatty acids / coumarin metabolic process / 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 ...coumarin 7-hydroxylase activity / Fatty acids / coumarin metabolic process / 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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / (S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE / Cytochrome P450 2A13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 2A13
B: Cytochrome P450 2A13
C: Cytochrome P450 2A13
D: Cytochrome P450 2A13
E: Cytochrome P450 2A13
F: Cytochrome P450 2A13
G: Cytochrome P450 2A13
H: Cytochrome P450 2A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)444,11121
Polymers438,4388
Non-polymers5,67313
Water88349
1
A: Cytochrome P450 2A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5833
Polymers54,8051
Non-polymers7792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 2A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5833
Polymers54,8051
Non-polymers7792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cytochrome P450 2A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5833
Polymers54,8051
Non-polymers7792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cytochrome P450 2A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5833
Polymers54,8051
Non-polymers7792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Cytochrome P450 2A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4212
Polymers54,8051
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Cytochrome P450 2A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4212
Polymers54,8051
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Cytochrome P450 2A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4212
Polymers54,8051
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Cytochrome P450 2A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5133
Polymers54,8051
Non-polymers7092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.657, 120.324, 153.731
Angle α, β, γ (deg.)100.62, 101.82, 93.73
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Cytochrome P450 2A13 / CYPIIA13


Mass: 54804.758 Da / Num. of mol.: 8 / 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 / Heme B


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-NCT / (S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE / (S)-(-)-NICOTINE / 3-[(2S)-1-METHYL-2-PYRROLIDINYL] PYRIDINE / Nicotine


Mass: 162.232 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N2 / Comment: alkaloid*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.89 Å3/Da / Density % sol: 57.46 %
Crystal growTemperature: 298 K / pH: 8.5
Details: 30% PEG 3350, 0.175 M Tris, and 0.2 M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2010
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→117.59 Å / Num. obs: 164366 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.067 / Rsym value: 0.094 / Net I/σ(I): 7.1
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.641 / % possible all: 88.1

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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 1Z10

1z10


Resolution: 2.5→102.58 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.875 / SU B: 10.561 / SU ML: 0.239 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.55 / ESU R Free: 0.332
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.285 8224 5 %RANDOM
Rwork0.224 ---
obs0.228 156132 96.7 %-
all-156132 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.11 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0.01 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→102.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30027 0 398 49 30474
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d1.692
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 491 -
Rwork0.286 9569 -
obs--79.21 %

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