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- PDB-9duj: Crystal structure of RufO in complex with (Nle)RYLH -

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Basic information

Entry
Database: PDB / ID: 9duj
TitleCrystal structure of RufO in complex with (Nle)RYLH
Components
  • Cytochrome P450
  • NLE-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
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesStreptomyces atratus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 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
DepositionOct 3, 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: NLE-ARG-TYR-LEU-HIS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,21810
Polymers44,1462
Non-polymers1,0728
Water9,296516
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-43 kcal/mol
Surface area16250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.258, 77.833, 89.178
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Cytochrome P450


Mass: 43442.914 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 NLE-ARG-TYR-LEU-HIS


Mass: 702.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptomyces atratus (bacteria)

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Non-polymers , 5 types, 524 molecules

#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.62 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 3000, 100 mM Tris base/HCl pH 7.0, 200 mM Calcium acetate

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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: Sep 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.51→50 Å / Num. obs: 62065 / % possible obs: 100 % / Redundancy: 12.3 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.035 / Rrim(I) all: 0.124 / Χ2: 2.312 / Net I/σ(I): 9.5 / Num. measured all: 760297
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.51-1.5410.50.63130510.9250.980.1990.6620.859100
1.54-1.56120.60930480.9440.9850.1770.6350.899100
1.56-1.5913.20.55730940.9640.9910.1560.5790.989100
1.59-1.6313.30.50530520.9680.9920.1410.5251.104100
1.63-1.6613.40.46230640.9720.9930.1290.481.161100
1.66-1.713.30.41430840.9730.9930.1160.431.313100
1.7-1.7413.30.36130540.9790.9950.1020.3761.49100
1.74-1.7913.10.31430670.9820.9950.090.3271.695100
1.79-1.8412.80.27430780.9850.9960.0790.2861.804100
1.84-1.912.70.24330690.9870.9970.0710.2532.034100
1.9-1.97120.20830650.9910.9980.0630.2172.265100
1.97-2.0510.80.1831130.9910.9980.0580.1892.593100
2.05-2.1411.20.14830870.9930.9980.0470.1552.872100
2.14-2.2612.60.13130850.9950.9990.0380.1373.087100
2.26-2.412.80.11331240.9960.9990.0330.1183.296100
2.4-2.5812.50.10131180.9970.9990.030.1053.48100
2.58-2.8412.30.09131250.9970.9990.0270.0953.752100
2.84-3.2511.60.07931520.9970.9990.0240.0834.066100
3.25-4.19.60.06731950.9980.9990.0220.0714.29799.9
4.1-5012.10.05933400.99810.0170.0623.77299.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
SCALEPACKdata scaling
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→47.58 Å / SU ML: 0.14 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 18.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1908 1999 3.23 %
Rwork0.1638 --
obs0.1646 61898 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.51→47.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3088 0 29 516 3633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053266
X-RAY DIFFRACTIONf_angle_d0.874482
X-RAY DIFFRACTIONf_dihedral_angle_d13.2471208
X-RAY DIFFRACTIONf_chiral_restr0.05491
X-RAY DIFFRACTIONf_plane_restr0.009601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.550.20691330.18973999X-RAY DIFFRACTION94
1.55-1.590.22211430.17444243X-RAY DIFFRACTION100
1.59-1.640.2141410.16974241X-RAY DIFFRACTION100
1.64-1.690.19351420.16434275X-RAY DIFFRACTION100
1.69-1.750.19021420.16494246X-RAY DIFFRACTION100
1.75-1.820.19651440.16554291X-RAY DIFFRACTION100
1.82-1.90.20971400.17334227X-RAY DIFFRACTION100
1.9-20.23381430.16574293X-RAY DIFFRACTION100
2-2.130.19861430.15934253X-RAY DIFFRACTION100
2.13-2.290.18151440.15684327X-RAY DIFFRACTION100
2.29-2.520.20271440.16434306X-RAY DIFFRACTION100
2.52-2.890.18741440.16624337X-RAY DIFFRACTION100
2.89-3.640.17381460.16164335X-RAY DIFFRACTION99
3.64-47.580.17321500.15954526X-RAY DIFFRACTION99

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