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- PDB-2p85: Structure of Human Lung Cytochrome P450 2A13 with indole bound in... -

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Basic information

Entry
Database: PDB / ID: 2p85
TitleStructure of Human Lung Cytochrome P450 2A13 with indole bound in two alternate conformations
ComponentsCytochrome P450 2A13
KeywordsOXIDOREDUCTASE / CYP2A13 / P450 2A13 / P450 / monooxygenase / nicotine oxidase / coumarine 7-hydroxylase / NNK oxidase / 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone oxidase / heme
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 / INDOLE / Cytochrome P450 2A13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsScott, E.E. / Stout, C.D.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structure of the human lung cytochrome P450 2A13.
Authors: Smith, B.D. / Sanders, J.L. / Porubsky, P.R. / Lushington, G.H. / Stout, C.D. / Scott, E.E.
History
DepositionMar 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 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 1.4Aug 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

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,93324
Polymers328,8296
Non-polymers5,10518
Water10,755597
1
A: Cytochrome P450 2A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6564
Polymers54,8051
Non-polymers8513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 2A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6564
Polymers54,8051
Non-polymers8513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P450 2A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6564
Polymers54,8051
Non-polymers8513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome P450 2A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6564
Polymers54,8051
Non-polymers8513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Cytochrome P450 2A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6564
Polymers54,8051
Non-polymers8513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Cytochrome P450 2A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6564
Polymers54,8051
Non-polymers8513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.320, 110.280, 142.000
Angle α, β, γ (deg.)90.00, 110.28, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-874-

HOH

21A-935-

HOH

31E-1189-

HOH

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Components

#1: Protein
Cytochrome P450 2A13 / CYPIIA13


Mass: 54804.758 Da / Num. of mol.: 6 / Fragment: catalytic domain (Residues 29-494) / Mutation: V23M, W24A, R25K, Q26K, R27T, K28S, R30K
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.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-IND / INDOLE / Indole


Mass: 117.148 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C8H7N
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 597 / 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: 2.71 Å3/Da / Density % sol: 54.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Ammonium Sulfate, Hepes, PEG 2000 monomethyl ether , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 22, 2005
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionHighest resolution: 2.35 Å / Num. obs: 142896 / Redundancy: 4.7 % / Biso Wilson estimate: 36.2 Å2 / Net I/σ(I): 14.5
Reflection shellHighest resolution: 2.35 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.431 / % possible all: 97.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
Blu-Icedata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SUO

1suo


Resolution: 2.35→29.34 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1849573.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 14034 9.9 %RANDOM
Rwork0.219 ---
obs0.219 141889 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.6015 Å2 / ksol: 0.353435 e/Å3
Displacement parametersBiso mean: 45.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.88 Å20 Å24.05 Å2
2---3.88 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.35→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22578 0 366 597 23541
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.882
X-RAY DIFFRACTIONc_mcangle_it2.782.5
X-RAY DIFFRACTIONc_scbond_it4.564
X-RAY DIFFRACTIONc_scangle_it5.715
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.347 2332 9.9 %
Rwork0.293 21262 -
obs--97.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3xdict_heme.parxdict_heme.top
X-RAY DIFFRACTION4indole.parindole.top

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