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- PDB-4rui: Crystal structure of a cytochrome P450 2A6 in complex with a mono... -

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Basic information

Entry
Database: PDB / ID: 4rui
TitleCrystal structure of a cytochrome P450 2A6 in complex with a monoterpene - sabinene.
ComponentsCytochrome P450 2A6
KeywordsOXIDOREDUCTASE / P450 / CYTOCHROME P450 2A6 / MONOOXYGENASE / MEMBRANE PROTEIN / CYP2A6 / ENDOPLASMIC RETICULUM / HEME / IRON / MEMBRANE / METAL BINDING / MICROSOME
Function / homology
Function and homology information


coumarin catabolic process / coumarin 7-hydroxylase activity / 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 / 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 / steroid metabolic process ...coumarin catabolic process / coumarin 7-hydroxylase activity / 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 / 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 / steroid metabolic process / xenobiotic catabolic process / cytoplasmic microtubule / xenobiotic metabolic process / 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 / Sabinene / Cytochrome P450 2A6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsShah, M.B. / Stout, C.D. / Halpert, J.R.
CitationJournal: Mol.Pharmacol. / Year: 2015
Title: Structural and Biophysical Characterization of Human Cytochromes P450 2B6 and 2A6 Bound to Volatile Hydrocarbons: Analysis and Comparison.
Authors: Shah, M.B. / Wilderman, P.R. / Liu, J. / Jang, H.H. / Zhang, Q. / Stout, C.D. / Halpert, J.R.
History
DepositionNov 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_auth_seq_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
Revision 1.3May 22, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)332,54618
Polymers328,0306
Non-polymers4,51612
Water5,621312
1
D: Cytochrome P450 2A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4243
Polymers54,6721
Non-polymers7532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Cytochrome P450 2A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4243
Polymers54,6721
Non-polymers7532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Cytochrome P450 2A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4243
Polymers54,6721
Non-polymers7532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Cytochrome P450 2A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4243
Polymers54,6721
Non-polymers7532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Cytochrome P450 2A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4243
Polymers54,6721
Non-polymers7532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Cytochrome P450 2A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4243
Polymers54,6721
Non-polymers7532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.740, 132.970, 133.030
Angle α, β, γ (deg.)62.40, 99.06, 80.93
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21A
12D
22B
13D
23C
14D
24E
15D
25F
16A
26B
17A
27C
18A
28E
19A
29F
110B
210C
111B
211E
112B
212F
113C
213E
114C
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPRODA31 - 4939 - 471
21PROPROAB31 - 4939 - 471
12HISHISDA31 - 4959 - 473
22HISHISBC31 - 4959 - 473
13PROPRODA31 - 4939 - 471
23PROPROCD31 - 4939 - 471
14HISHISDA31 - 4959 - 473
24HISHISEE31 - 4959 - 473
15HISHISDA31 - 4959 - 473
25HISHISFF31 - 4959 - 473
16PROPROAB31 - 4939 - 471
26PROPROBC31 - 4939 - 471
17ARGARGAB31 - 4949 - 472
27ARGARGCD31 - 4949 - 472
18PROPROAB31 - 4939 - 471
28PROPROEE31 - 4939 - 471
19PROPROAB31 - 4939 - 471
29PROPROFF31 - 4939 - 471
110PROPROBC31 - 4939 - 471
210PROPROCD31 - 4939 - 471
111HISHISBC31 - 4959 - 473
211HISHISEE31 - 4959 - 473
112HISHISBC31 - 4959 - 473
212HISHISFF31 - 4959 - 473
113PROPROCD31 - 4939 - 471
213PROPROEE31 - 4939 - 471
114PROPROCD31 - 4939 - 471
214PROPROFF31 - 4939 - 471
115HISHISEE31 - 4959 - 473
215HISHISFF31 - 4959 - 473

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
DetailsThe crystal structure contains 6 identical chains, chain A through chain F in the asymmetric unit.

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Components

#1: Protein
Cytochrome P450 2A6 / 1 / 4-cineole 2-exo-monooxygenase / CYPIIA6 / Coumarin 7-hydroxylase / Cytochrome P450 IIA3 / ...1 / 4-cineole 2-exo-monooxygenase / CYPIIA6 / Coumarin 7-hydroxylase / Cytochrome P450 IIA3 / Cytochrome P450(I)


Mass: 54671.637 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Remark: The residues 1-28 of the corresponding database sequence (UNP P11509) were replaced with the sequence MAKKTS. MET A 23 UNP P11509 SEE REMARK ALA A 24 UNP P11509 SEE REMARK LYS A 25 ...Details: Remark: The residues 1-28 of the corresponding database sequence (UNP P11509) were replaced with the sequence MAKKTS. MET A 23 UNP P11509 SEE REMARK ALA A 24 UNP P11509 SEE REMARK LYS A 25 UNP P11509 SEE REMARK LYS A 26 UNP P11509 SEE REMARK THR A 27 UNP P11509 SEE REMARK SER A 28 UNP P11509 SEE REMARK HIS A 495 UNP P11509 EXPRESSION TAG HIS A 496 UNP P11509 EXPRESSION TAG HIS A 497 UNP P11509 EXPRESSION TAG HIS A 498 UNP P11509 EXPRESSION TAG
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP2A3, CYP2A6 / Plasmid: pCW / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: P11509, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-SNE / Sabinene / (1S,5S)-4-methylidene-1-(propan-2-yl)bicyclo[3.1.0]hexane


Mass: 136.234 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.86 Å3/Da / Density % sol: 56.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.3 M sodium acetate, 0.1 M sodium cacodylate, and 25% w/v PEG 2K MME, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 28, 2013
RadiationMonochromator: Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.61→113.76 Å / Num. all: 122464 / Num. obs: 110464 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.53 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 4.7
Reflection shellResolution: 2.61→2.67 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 1.2 / % possible all: 65.7

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.61→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.914 / Redundancy reflection obs: 3.53 / SU B: 15.674 / SU ML: 0.303 / Cross valid method: THROUGHOUT / ESU R: 1.347 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26071 5003 5 %RANDOM
Rwork0.19658 ---
all0.19976 104918 --
obs0.19976 94636 90.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.24 Å2
Baniso -1Baniso -2Baniso -3
1-3.17 Å20.47 Å2-0.42 Å2
2---1.26 Å20.5 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.61→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21885 0 318 312 22515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01922772
X-RAY DIFFRACTIONr_bond_other_d0.0060.0221028
X-RAY DIFFRACTIONr_angle_refined_deg1.611.97430913
X-RAY DIFFRACTIONr_angle_other_deg1.191348164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.57252782
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78923.5141087
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.901153635
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.61315161
X-RAY DIFFRACTIONr_chiral_restr0.0860.23301
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02126181
X-RAY DIFFRACTIONr_gen_planes_other0.0060.025657
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11D296370.05
12A296370.05
21D299470.05
22B299470.05
31D282410.06
32C282410.06
41D282290.06
42E282290.06
51D282390.05
52F282390.05
61A297490.04
62B297490.04
71A283060.06
72C283060.06
81A281170.06
82E281170.06
91A280320.05
92F280320.05
101B282080.05
102C282080.05
111B282140.06
112E282140.06
121B282410.05
122F282410.05
131C275240.06
132E275240.06
141C277740.05
142F277740.05
151E278500.05
152F278500.05
LS refinement shellResolution: 2.609→2.677 Å / Total num. of bins used: 20 / Redundancy reflection obs: 2.5
RfactorNum. reflection% reflection
Rfree0.4 262 -
Rwork0.36 4543 -
obs-4543 59.45 %

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