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- PDB-9km6: The crystal structure of XhnM1 and its inhibitor sinefugin -

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Basic information

Entry
Database: PDB / ID: 9km6
TitleThe crystal structure of XhnM1 and its inhibitor sinefugin
ComponentsClass I SAM-dependent methyltransferase
KeywordsTRANSFERASE / complex / inhibitor / sinefugin
Function / homologyMethyltransferase domain 25 / Methyltransferase domain / biosynthetic process / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / SINEFUNGIN / Class I SAM-dependent methyltransferase
Function and homology information
Biological speciesStreptomyces xinghaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.00003128301 Å
AuthorsWu, L. / Tang, G.L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Targeted Discovery and Characterization of Type-II PKS-NRPS Hybrid DNA-Alkylating Antibiotics.
Authors: Nie, Q.Y. / Fang, S.Q. / Wu, L. / Gao, R.Q. / Hu, Y. / Ding, D. / Pan, H.X. / Pei, Z.F. / He, J.B. / Zhou, Q. / Chen, Z.H. / Hou, X.F. / Zhao, X.Q. / Tang, G.L.
History
DepositionNov 15, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Class I SAM-dependent methyltransferase
B: Class I SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,38911
Polymers64,1522
Non-polymers1,2389
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-45 kcal/mol
Surface area21700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.020, 147.020, 128.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein Class I SAM-dependent methyltransferase


Mass: 32075.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces xinghaiensis (bacteria) / Gene: Sfr7A_13950, SFRA_005385 / Production host: Escherichia coli B (bacteria) / References: UniProt: A0A3R7FZU3
#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.71 Å3/Da / Density % sol: 54.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: .01 M sodium chloride, 1.5 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→51.98 Å / Num. obs: 47707 / % possible obs: 100 % / Redundancy: 26.1 % / Biso Wilson estimate: 36.5812247044 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.083 / Net I/σ(I): 26.1
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 1.518 / Num. unique obs: 3461 / CC1/2: 0.836

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.00003128301→51.979419485 Å / SU ML: 0.242640284141 / Cross valid method: FREE R-VALUE / σ(F): 1.34640348899 / Phase error: 25.2935158279
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.236415982384 2346 4.91823899371 %
Rwork0.200907483481 45354 -
obs0.202665974044 47700 99.9497108373 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.7978605113 Å2
Refinement stepCycle: LAST / Resolution: 2.00003128301→51.979419485 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3866 0 81 254 4201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002169299785994045
X-RAY DIFFRACTIONf_angle_d0.5793713721355511
X-RAY DIFFRACTIONf_chiral_restr0.0429997697501590
X-RAY DIFFRACTIONf_plane_restr0.00436751136853748
X-RAY DIFFRACTIONf_dihedral_angle_d16.71949512832383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0000313-2.04090.3106037077371370.2717727835542642X-RAY DIFFRACTION100
2.0409-2.08520.3084760906651350.2744183907412602X-RAY DIFFRACTION99.8176513494
2.0852-2.13370.2813983165831280.2471060711672660X-RAY DIFFRACTION100
2.1337-2.18710.2941853346331430.2327245551172637X-RAY DIFFRACTION99.9640417116
2.1871-2.24620.2674125933761300.2310775641762622X-RAY DIFFRACTION99.9273783588
2.2462-2.31230.2482598583571240.2408299790322650X-RAY DIFFRACTION99.8560115191
2.3123-2.3870.2899697184071430.2316998061762646X-RAY DIFFRACTION100
2.387-2.47230.2959077092111460.2367632622572632X-RAY DIFFRACTION100
2.4723-2.57130.3014745905661480.2347537054232640X-RAY DIFFRACTION100
2.5713-2.68830.2776808246011420.2415861519972638X-RAY DIFFRACTION100
2.6883-2.830.2577499025011310.2313597160592673X-RAY DIFFRACTION100
2.83-3.00730.2989257333141330.2303503662132677X-RAY DIFFRACTION100
3.0073-3.23950.2475613162681350.2179683721472662X-RAY DIFFRACTION100
3.2395-3.56540.2229041432151500.2011766708142677X-RAY DIFFRACTION99.9293036409
3.5654-4.08110.2324310377161190.1751757948772739X-RAY DIFFRACTION100
4.0811-5.14110.1889879266981490.1565189644522712X-RAY DIFFRACTION100
5.1411-51.9790.1909155695131530.176347726712845X-RAY DIFFRACTION99.6675531915

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