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- PDB-7dls: Cytochrome P450 (CYP105D18) complex with papaverine -

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Basic information

Entry
Database: PDB / ID: 7dls
TitleCytochrome P450 (CYP105D18) complex with papaverine
ComponentsCytochrome P450 hydroxylase
KeywordsTRANSFERASE / papaverine N-oxide / eukaryotic cytochrome P450 / chemical modification / heme oxidation
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / 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
1-(3,4-DIMETHOXYBENZYL)-6,7-DIMETHOXYISOQUINOLINE / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 hydroxylase
Similarity search - Component
Biological speciesStreptomyces laurentii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsDo, H. / Lee, J.H.
CitationJournal: Iucrj / Year: 2021
Title: Characterization of high-H 2 O 2 -tolerant bacterial cytochrome P450 CYP105D18: insights into papaverine N-oxidation.
Authors: Pardhe, B.D. / Do, H. / Jeong, C.S. / Kim, K.H. / Lee, J.H. / Oh, T.J.
History
DepositionNov 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3593
Polymers44,4031
Non-polymers9562
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Superdex 200 10/300 GL column
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-26 kcal/mol
Surface area16480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.522, 52.172, 87.896
Angle α, β, γ (deg.)90.000, 110.680, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cytochrome P450 hydroxylase


Mass: 44403.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces laurentii (bacteria) / Gene: SLA_5925 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A160P685
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EV1 / 1-(3,4-DIMETHOXYBENZYL)-6,7-DIMETHOXYISOQUINOLINE / Papaverine


Mass: 339.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl, pH 8.5, 1.5 M Ammonium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 41490 / % possible obs: 94.15 % / Redundancy: 4.7 % / CC1/2: 1 / Net I/σ(I): 17.05
Reflection shellResolution: 2.06→2.1 Å / CC1/2: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DI3

7di3


Resolution: 2.06→44.59 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.128 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.225 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2184 1127 5 %RANDOM
Rwork0.1722 ---
obs0.1744 21580 94.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.61 Å2 / Biso mean: 32.834 Å2 / Biso min: 14.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.01 Å2
2---0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2.06→44.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3011 0 68 144 3223
Biso mean--31.98 37.27 -
Num. residues----392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133156
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172988
X-RAY DIFFRACTIONr_angle_refined_deg1.5751.6684317
X-RAY DIFFRACTIONr_angle_other_deg1.2911.5836843
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5155390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.33120.345174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36315476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9151533
X-RAY DIFFRACTIONr_chiral_restr0.070.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023638
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02740
LS refinement shellResolution: 2.064→2.117 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 81 -
Rwork0.254 1433 -
all-1514 -
obs--84.68 %

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