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- PDB-9eby: Crystal structure of RufO in complex with MRYLH -

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Basic information

Entry
Database: PDB / ID: 9eby
TitleCrystal structure of RufO in complex with MRYLH
Components
  • Cytochrome P450
  • MET-ARG-TYR-LEU-HIS
KeywordsOXIDOREDUCTASE / Rufomycin biosynthesis / cytochrome P450 enzyme / RiPP-producing enzyme / nitrating heme enzyme / peptide bound
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 / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsNolan, K. / Wang, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM147510 United States
CitationJournal: Acs Catalysis / Year: 2025
Title: Molecular Basis for Peptide Nitration by a Novel Cytochrome P450 Enzyme in RiPP Biosynthesis.
Authors: Nolan, K. / Usai, R. / Li, B. / Jordan, S. / Wang, Y.
History
DepositionNov 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2025Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450
B: MET-ARG-TYR-LEU-HIS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9075
Polymers44,1072
Non-polymers8013
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-35 kcal/mol
Surface area15970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.163, 79.300, 88.511
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytochrome P450


Mass: 43385.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces atratus (bacteria) / Gene: rufO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A224AU14
#2: Protein/peptide MET-ARG-TYR-LEU-HIS


Mass: 720.883 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptomyces atratus (bacteria)
#3: 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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.17 Å3/Da / Density % sol: 43.19 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: 18% PEG 3350, 0.2 M sodium tartrate dibasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Nov 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 24219 / % possible obs: 93.4 % / Redundancy: 5.2 % / CC1/2: 0.981 / CC star: 0.995 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.08 / Rrim(I) all: 0.19 / Χ2: 0.847 / Net I/σ(I): 6.2 / Num. measured all: 124813
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.03-2.074.10.73810760.5080.8210.3910.840.47184.1
2.07-2.14.30.66210690.5880.8610.3460.7510.51985
2.1-2.144.30.60610750.6060.8690.3160.6870.51984.6
2.14-2.194.40.56711040.6750.8980.2930.6410.49985.9
2.19-2.234.20.53810900.670.8960.2850.6130.52886.3
2.23-2.294.40.53311210.6660.8940.2710.6010.52987.5
2.29-2.344.70.47111560.740.9220.2370.5310.59790
2.34-2.414.90.45211650.7630.930.2210.5060.62990.8
2.41-2.485.40.42912480.7890.9390.20.4750.62697.4
2.48-2.565.60.37512280.8630.9620.1720.4140.6396.9
2.56-2.655.60.31912400.8980.9730.1470.3520.65796.2
2.65-2.765.70.27512480.9110.9760.1260.3040.70896.4
2.76-2.885.70.22212230.9480.9870.1010.2440.76595.9
2.88-3.035.70.19112460.9490.9870.0870.2110.84196
3.03-3.225.70.16212700.9710.9930.0730.1781.01697.1
3.22-3.475.50.13612840.9790.9950.0620.151.0898.7
3.47-3.825.10.12312940.9750.9940.0580.1371.38599.2
3.82-4.374.70.10813160.9820.9950.0540.1211.36899.2
4.37-5.5160.10113340.9880.9970.0440.1111.24499.3
5.51-506.20.1114320.9880.9970.0470.121.33899.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
SCALEPACKdata scaling
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→45.28 Å / SU ML: 0.28 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 24.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2621 2000 8.28 %
Rwork0.2031 --
obs0.208 24147 93.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.03→45.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3078 0 12 195 3285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093179
X-RAY DIFFRACTIONf_angle_d1.0494353
X-RAY DIFFRACTIONf_dihedral_angle_d9.609444
X-RAY DIFFRACTIONf_chiral_restr0.054476
X-RAY DIFFRACTIONf_plane_restr0.011581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.080.36821260.27631394X-RAY DIFFRACTION84
2.08-2.130.33061260.24531402X-RAY DIFFRACTION84
2.13-2.20.29611300.21961428X-RAY DIFFRACTION86
2.2-2.270.27621300.22011457X-RAY DIFFRACTION87
2.27-2.350.28671350.22321490X-RAY DIFFRACTION89
2.35-2.440.3241410.21881552X-RAY DIFFRACTION94
2.44-2.550.30011480.21421640X-RAY DIFFRACTION97
2.55-2.690.27721470.2071632X-RAY DIFFRACTION97
2.69-2.860.26311460.20141611X-RAY DIFFRACTION96
2.86-3.080.28561470.2031631X-RAY DIFFRACTION96
3.08-3.390.27151500.21191666X-RAY DIFFRACTION98
3.39-3.880.2211540.18181703X-RAY DIFFRACTION99
3.88-4.880.22251540.17321711X-RAY DIFFRACTION99
4.88-45.280.23721660.20361830X-RAY DIFFRACTION100

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