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- PDB-3ua1: Crystal structure of the cytochrome P4503A4-bromoergocryptine complex -

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Basic information

Entry
Database: PDB / ID: 3ua1
TitleCrystal structure of the cytochrome P4503A4-bromoergocryptine complex
ComponentsCytochrome P450 3A4CYP3A4
KeywordsOXIDOREDUCTASE / Protein-substrate complex / monooxygenase / cytochrome P450 reductase / cytochrome b5 / membrane
Function / homology
Function and homology information


quinine 3-monooxygenase / 1,8-cineole 2-exo-monooxygenase / albendazole monooxygenase (sulfoxide-forming) / quinine 3-monooxygenase activity / 1,8-cineole 2-exo-monooxygenase activity / 1-alpha,25-dihydroxyvitamin D3 23-hydroxylase activity / vitamin D3 25-hydroxylase activity / testosterone 6-beta-hydroxylase activity / vitamin D 24-hydroxylase activity / vitamin D catabolic process ...quinine 3-monooxygenase / 1,8-cineole 2-exo-monooxygenase / albendazole monooxygenase (sulfoxide-forming) / quinine 3-monooxygenase activity / 1,8-cineole 2-exo-monooxygenase activity / 1-alpha,25-dihydroxyvitamin D3 23-hydroxylase activity / vitamin D3 25-hydroxylase activity / testosterone 6-beta-hydroxylase activity / vitamin D 24-hydroxylase activity / vitamin D catabolic process / retinoic acid 4-hydroxylase activity / aflatoxin metabolic process / caffeine oxidase activity / estrogen 16-alpha-hydroxylase activity / estrogen 2-hydroxylase activity / lipid hydroxylation / alkaloid catabolic process / anandamide 8,9 epoxidase activity / anandamide 11,12 epoxidase activity / anandamide 14,15 epoxidase activity / : / Aflatoxin activation and detoxification / Biosynthesis of maresin-like SPMs / monoterpenoid metabolic process / vitamin D metabolic process / Atorvastatin ADME / steroid catabolic process / Xenobiotics / oxidative demethylation / steroid hydroxylase activity / Phase I - Functionalization of compounds / long-chain fatty acid biosynthetic process / estrogen metabolic process / retinoic acid metabolic process / retinol metabolic process / Prednisone ADME / unspecific monooxygenase / aromatase activity / Aspirin ADME / steroid metabolic process / androgen metabolic process / xenobiotic catabolic process / cholesterol metabolic process / steroid binding / xenobiotic metabolic process / monooxygenase activity / lipid metabolic process / oxygen binding / oxidoreductase activity / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / enzyme binding / cytoplasm
Similarity search - Function
Cytochrome P450, E-class, group II / Cytochrome P450, E-class, CYP3A / 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
bromoergocryptine / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 3A4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSevrioukova, I.F. / Poulos, T.L.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural and Mechanistic Insights into the Interaction of Cytochrome P4503A4 with Bromoergocryptine, a Type I Ligand.
Authors: Sevrioukova, I.F. / Poulos, T.L.
History
DepositionOct 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Feb 15, 2012Group: Database references
Revision 1.3Jun 28, 2017Group: Database references / Source and taxonomy
Category: entity_src_gen / struct_ref ...entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num ..._entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_seq_type
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Cytochrome P450 3A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0293
Polymers55,7581
Non-polymers1,2712
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.670, 99.390, 131.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Cytochrome P450 3A4 / CYP3A4 / Albendazole monooxygenase / Albendazole sulfoxidase / CYPIIIA3 / CYPIIIA4 / Cytochrome P450 3A3 / ...Albendazole monooxygenase / Albendazole sulfoxidase / CYPIIIA3 / CYPIIIA4 / Cytochrome P450 3A3 / Cytochrome P450 HLp / Cytochrome P450 NF-25 / Cytochrome P450-PCN1 / Nifedipine oxidase / Quinine 3-monooxygenase / Taurochenodeoxycholate 6-alpha-hydroxylase


Mass: 55757.812 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP3A4, CYP3A3 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P08684, EC: 1.14.13.32, EC: 1.14.13.67, EC: 1.14.13.97
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-08Y / bromoergocryptine / bromocriptine / Bromocriptine


Mass: 654.594 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H40BrN5O5 / Comment: agonist*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsUNP RESIDUES 3-22 WERE DELETED DURING CLONING.

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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: 2.2 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 293 K / Method: microbatch under oil / pH: 6.4
Details: 2% tacsimate, 6% PEG3350, pH 6.4, MICROBATCH UNDER OIL, temperature 293K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2010 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→39.898 Å / Num. all: 28144 / Num. obs: 27255 / % possible obs: 97.2 % / Redundancy: 5.3 % / Biso Wilson estimate: 36.2 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 12.1
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3721 / % possible all: 92.2

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TGN

1tgn


Resolution: 2.15→39.898 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.919 / Occupancy max: 1 / Occupancy min: 1 / SU B: 15.429 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.293 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2779 1383 5.1 %RANDOM
Rwork0.2207 25874 --
obs0.2236 27255 96.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 73.51 Å2 / Biso mean: 52.594 Å2 / Biso min: 16.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.04 Å20 Å20 Å2
2---2 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.15→39.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3672 0 86 65 3823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223861
X-RAY DIFFRACTIONr_angle_refined_deg1.5842.0375249
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1425452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.60624160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.23515686
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6131520
X-RAY DIFFRACTIONr_chiral_restr0.1050.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212865
X-RAY DIFFRACTIONr_mcbond_it0.7171.52288
X-RAY DIFFRACTIONr_mcangle_it1.31223743
X-RAY DIFFRACTIONr_scbond_it1.95531573
X-RAY DIFFRACTIONr_scangle_it3.0494.51506
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 100 -
Rwork0.278 1784 -
all-1884 -
obs--91.77 %
Refinement TLS params.Method: refined / Origin x: 19.2792 Å / Origin y: 23.0642 Å / Origin z: -14.1652 Å
111213212223313233
T0.101 Å2-0.0116 Å2-0.072 Å2-0.1077 Å20.0274 Å2--0.0923 Å2
L1.0153 °2-1.1025 °20.3496 °2-2.3862 °2-0.4271 °2--0.8519 °2
S-0.189 Å °0.0442 Å °0.0826 Å °0.2637 Å °0.0257 Å °0.0464 Å °-0.1485 Å °0.0108 Å °0.1633 Å °

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