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- PDB-9p3b: Structure of radical S-adenosylmethionine methyltransferase, NocN... -

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Basic information

Entry
Database: PDB / ID: 9p3b
TitleStructure of radical S-adenosylmethionine methyltransferase, NocN, from Nocardia with two SAM and [4Fe-4S] cluster bound
Componentsradical S-adenosylmethionine methyltransferase NocN
KeywordsOXIDOREDUCTASE / radical S-adenosylmethionine / nosiheptide / nocathiacin
Function / homology
Function and homology information


porphyrin-containing compound biosynthetic process / catalytic activity / 4 iron, 4 sulfur cluster binding / cytoplasm
Similarity search - Function
3-Methyl-2-indolic acid methyltransferase, NocN/NosN-like / Anaerobic coproporphyrinogen-III oxidase / Radical SAM, alpha/beta horseshoe / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / : / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM
Similarity search - Domain/homology
HEXANE-1,6-DIOL / IMIDAZOLE / S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / Heme chaperone HemW
Similarity search - Component
Biological speciesNocardia sp. ATCC 202099 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsWang, B. / Knox, H.L. / York, N.J. / Radle, M.I. / Silakov, A. / Booker, S.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-122595 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2026
Title: Structural and Spectroscopic Basis for Catalysis by a Class C Radical S-Adenosylmethionine Methylase Involved in Nosiheptide/Nocathiacin Biosynthesis
Authors: Wang, B. / Knox, H.L. / York, N.J. / Radle, M.I. / Silakov, A. / Booker, S.J.
History
DepositionJun 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: radical S-adenosylmethionine methyltransferase NocN
B: radical S-adenosylmethionine methyltransferase NocN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,59413
Polymers92,7552
Non-polymers2,83911
Water12,106672
1
A: radical S-adenosylmethionine methyltransferase NocN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9508
Polymers46,3781
Non-polymers1,5727
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: radical S-adenosylmethionine methyltransferase NocN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6445
Polymers46,3781
Non-polymers1,2674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.905, 86.223, 145.031
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein radical S-adenosylmethionine methyltransferase NocN / Heme chaperone HemW


Mass: 46377.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardia sp. ATCC 202099 (bacteria) / Gene: nocN / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E5DUI5

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Non-polymers , 5 types, 683 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2
#4: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 672 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.11 Å3/Da / Density % sol: 41.75 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 100 mM Hepes pH 7.5, 100 mM Li2SO4, 100 mM MgCl2, 20% w/v PEG 3350, and 10% w/v 1,6-hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 107057 / % possible obs: 100 % / Redundancy: 8.2 % / Rpim(I) all: 0.037 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.84-1.878.20.87833330.8360.9540.3220.9360.759100
1.87-1.918.20.72633190.8670.9640.2670.7740.786100
1.91-1.948.20.6133330.9120.9770.2240.6510.868100
1.94-1.988.20.47633710.9440.9850.1750.5080.818100
1.98-2.038.20.41233230.9520.9880.1510.4390.834100
2.03-2.078.20.35733310.960.990.1310.3810.876100
2.07-2.128.30.29833490.9690.9920.1090.3180.936100
2.12-2.188.30.26233420.9770.9940.0960.2790.898100
2.18-2.258.30.22733520.9810.9950.0830.2420.914100
2.25-2.328.30.20733660.9820.9950.0760.2211.044100
2.32-2.48.30.16933580.9870.9970.0620.180.876100
2.4-2.58.30.15233670.990.9980.0550.1610.889100
2.5-2.618.30.13633560.9910.9980.050.1450.947100
2.61-2.758.30.12233830.9920.9980.0450.131.017100
2.75-2.928.30.10734090.9940.9980.0390.1151.094100
2.92-3.158.30.09233700.9940.9990.0340.0991.171100
3.15-3.468.20.07434280.9960.9990.0270.0781.05100
3.46-3.968.20.06234400.9970.9990.0230.0671.037100
3.96-4.998.10.05334800.9980.9990.020.0570.907100
4.99-507.60.0536360.9960.9990.0190.0540.73899.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→41.32 Å / SU ML: 0.1843 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.8979
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2067 3053 2.85 %
Rwork0.1711 104004 -
obs0.1721 107057 82.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.64 Å2
Refinement stepCycle: LAST / Resolution: 1.83→41.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6173 0 161 672 7006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00726522
X-RAY DIFFRACTIONf_angle_d0.82048843
X-RAY DIFFRACTIONf_chiral_restr0.0565968
X-RAY DIFFRACTIONf_plane_restr0.00771141
X-RAY DIFFRACTIONf_dihedral_angle_d14.95632399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.860.2727760.25482371X-RAY DIFFRACTION41.99
1.86-1.890.2769880.23382839X-RAY DIFFRACTION49.38
1.89-1.920.2572900.22072977X-RAY DIFFRACTION52.06
1.92-1.960.2406980.20683148X-RAY DIFFRACTION54.8
1.96-20.2072950.19343301X-RAY DIFFRACTION58.49
2-2.040.2772910.19113631X-RAY DIFFRACTION62.7
2.04-2.080.21921090.18463927X-RAY DIFFRACTION68.52
2.08-2.130.22071150.18064268X-RAY DIFFRACTION74.63
2.13-2.180.17231330.17944644X-RAY DIFFRACTION81.21
2.18-2.240.23711450.17685058X-RAY DIFFRACTION87.83
2.24-2.310.23531480.18395285X-RAY DIFFRACTION93
2.31-2.380.17441660.185522X-RAY DIFFRACTION96.49
2.38-2.470.22351820.18135598X-RAY DIFFRACTION98.37
2.47-2.570.26111560.18075676X-RAY DIFFRACTION99.45
2.57-2.680.23381660.18235743X-RAY DIFFRACTION99.92
2.68-2.830.23081590.18555704X-RAY DIFFRACTION99.98
2.83-30.21341760.17745732X-RAY DIFFRACTION100
3-3.230.17951700.16785701X-RAY DIFFRACTION99.98
3.23-3.560.20421750.155731X-RAY DIFFRACTION100
3.56-4.070.18391620.14435746X-RAY DIFFRACTION99.98
4.08-5.130.16561880.14275687X-RAY DIFFRACTION100
5.13-41.320.21381650.17995715X-RAY DIFFRACTION99.73

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