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- PDB-8spc: Crystal structure of the cytochrome P450 enzyme RufO -

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Basic information

Entry
Database: PDB / ID: 8spc
TitleCrystal structure of the cytochrome P450 enzyme RufO
ComponentsCytochrome P450
KeywordsMETAL BINDING PROTEIN / RufO / Aromatic nitration / Cytochrome P450
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, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesStreptomyces atratus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 1.871 Å
AuthorsDratch, B.D. / Davis, K.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM147557 United States
CitationJournal: Acs Chem.Biol. / Year: 2023
Title: Insights into Substrate Recognition by the Unusual Nitrating Enzyme RufO.
Authors: Dratch, B.D. / McWhorter, K.L. / Blue, T.C. / Jones, S.K. / Horwitz, S.M. / Davis, K.M.
History
DepositionMay 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3246
Polymers45,5501
Non-polymers7745
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Size exclusion chromatography was performed with a standard of molecules with known molecular weights.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-39 kcal/mol
Surface area16390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.627, 77.627, 136.898
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytochrome P450 / RufO


Mass: 45550.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces atratus (bacteria) / Gene: rufO / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A224AU14

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Non-polymers , 5 types, 223 molecules

#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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.33 Å3/Da / Density % sol: 47.2 % / Description: red, cube
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 0.2 M magnesium chloride, 0.1 M Bis-Tris, 23% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 30, 2022
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.871→39.34 Å / Num. obs: 35269 / % possible obs: 99.56 % / Redundancy: 12.8 % / Biso Wilson estimate: 40.17 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.09647 / Rpim(I) all: 0.02792 / Rrim(I) all: 0.1005 / Net I/σ(I): 15.29
Reflection shellResolution: 1.871→1.937 Å / Redundancy: 8.4 % / Rmerge(I) obs: 1.469 / Mean I/σ(I) obs: 1.14 / Num. unique obs: 3398 / CC1/2: 0.687 / CC star: 0.903 / Rpim(I) all: 0.5285 / Rrim(I) all: 1.564 / % possible all: 96.32

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
Coot0.9.8.1model building
RefinementMethod to determine structure: SIR / Resolution: 1.871→39.34 Å / SU ML: 0.2309 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.5635
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2165 3197 9.08 %
Rwork0.1928 32002 -
obs0.195 35199 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.17 Å2
Refinement stepCycle: LAST / Resolution: 1.871→39.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2834 0 50 218 3102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00793019
X-RAY DIFFRACTIONf_angle_d0.84184147
X-RAY DIFFRACTIONf_chiral_restr0.0535460
X-RAY DIFFRACTIONf_plane_restr0.0166552
X-RAY DIFFRACTIONf_dihedral_angle_d14.36041095
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.871-1.90.3891280.35291293X-RAY DIFFRACTION93.24
1.9-1.930.36181360.30361372X-RAY DIFFRACTION100
1.93-1.960.32851300.26951363X-RAY DIFFRACTION99.93
1.96-1.990.29651520.25351371X-RAY DIFFRACTION100
1.99-2.030.27141270.23941353X-RAY DIFFRACTION99.93
2.03-2.070.30261330.23331381X-RAY DIFFRACTION99.93
2.07-2.110.25661480.22681364X-RAY DIFFRACTION99.8
2.11-2.160.26761290.21211382X-RAY DIFFRACTION99.87
2.16-2.210.24091330.20541378X-RAY DIFFRACTION100
2.21-2.260.20911460.19611357X-RAY DIFFRACTION99.8
2.26-2.320.22661390.18821376X-RAY DIFFRACTION99.93
2.32-2.390.23971330.19111386X-RAY DIFFRACTION99.87
2.39-2.470.26161420.19811373X-RAY DIFFRACTION99.8
2.47-2.560.21861420.20531387X-RAY DIFFRACTION100
2.56-2.660.25321310.22511397X-RAY DIFFRACTION100
2.66-2.780.23541390.22441401X-RAY DIFFRACTION100
2.78-2.930.27171450.21131385X-RAY DIFFRACTION100
2.93-3.110.2511310.21081415X-RAY DIFFRACTION99.94
3.11-3.350.25471430.20211411X-RAY DIFFRACTION100
3.35-3.690.17551480.18651410X-RAY DIFFRACTION99.94
3.69-4.220.17951440.15561429X-RAY DIFFRACTION100
4.22-5.320.15111520.15771447X-RAY DIFFRACTION100
5.32-39.340.20691460.18141571X-RAY DIFFRACTION99.94

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