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- PDB-7di3: Cytochrome P450 (CYP105D18) W.T. -

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Basic information

Entry
Database: PDB / ID: 7di3
TitleCytochrome P450 (CYP105D18) W.T.
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
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 hydroxylase
Similarity search - Component
Biological speciesStreptomyces laurentii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 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 18, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450 hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0202
Polymers44,4031
Non-polymers6161
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-25 kcal/mol
Surface area16500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.688, 52.444, 87.952
Angle α, β, γ (deg.)90.000, 110.820, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.23 Å3/Da / Density % sol: 44.73 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Lithium sulfate, 0.1 M Tris-HCl, pH 8.5, and 25 %(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 40181 / % possible obs: 96.9 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 29.4
Reflection shellResolution: 1.69→1.73 Å / Rmerge(I) obs: 0.36 / Num. unique obs: 3385

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UBS

4ubs


Resolution: 1.69→27.42 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.07 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 2211 5.2 %RANDOM
Rwork0.1659 ---
obs0.1683 40181 96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.6 Å2 / Biso mean: 26.024 Å2 / Biso min: 11.07 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.69→27.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2995 0 43 319 3357
Biso mean--16.82 34.98 -
Num. residues----381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133113
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172945
X-RAY DIFFRACTIONr_angle_refined_deg1.8031.6754251
X-RAY DIFFRACTIONr_angle_other_deg1.4151.5866754
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4995379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.79720.16187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.39615493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.751537
X-RAY DIFFRACTIONr_chiral_restr0.090.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023577
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02742
LS refinement shellResolution: 1.69→1.731 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.244 138 -
Rwork0.235 2470 -
obs--81.17 %

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