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- PDB-9klx: The complex structure of XhnM1 and Xinhaicarcin BG -

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Basic information

Entry
Database: PDB / ID: 9klx
TitleThe complex structure of XhnM1 and Xinhaicarcin BG
ComponentsClass I SAM-dependent methyltransferase
KeywordsTRANSFERASE / methyl group transferase / complex
Function / homologyMethyltransferase domain 25 / Methyltransferase domain / biosynthetic process / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / : / ACETATE ION / Class I SAM-dependent methyltransferase
Function and homology information
Biological speciesStreptomyces xinghaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.80000915376 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,9787
Polymers32,0761
Non-polymers9036
Water1,874104
1
A: Class I SAM-dependent methyltransferase
hetero molecules

A: Class I SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,95714
Polymers64,1522
Non-polymers1,80512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3520 Å2
ΔGint-49 kcal/mol
Surface area21100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.610, 51.090, 41.750
Angle α, β, γ (deg.)90.000, 96.300, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Class I SAM-dependent methyltransferase


Mass: 32075.934 Da / Num. of mol.: 1
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-A1EKQ / (S)-N-((2R,3S,3a'R,4R,11'S)-3-((2-amino-6-oxo-1,6-dihydro-7H-purin-7-yl)methyl)-3,7',11'-trihydroxy-5',8'-dioxo-3a',4,5,5',8',9',10',11'-octahydro-3H,3'H-spiro[furan-2,2'-furo[2,3,4-de]naphtho[2,3-h]chromen]-4-yl)-1-methylpiperidine-2-carboxamide


Mass: 701.683 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H35N7O10 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.11 Å3/Da / Density % sol: 41.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate trihydrate pH 4.5, 3.0 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.8→24.631 Å / Num. obs: 24877 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 29.668181938 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.9
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 1.005 / Num. unique obs: 1481 / CC1/2: 0.872

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.80000915376→24.6308969654 Å / SU ML: 0.210397127261 / Cross valid method: FREE R-VALUE / σ(F): 1.35059738547 / Phase error: 26.3960373647
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.222493504124 1181 4.75557703149 %
Rwork0.187102129284 23653 -
obs0.188810488445 24834 99.6229139923 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.9787568718 Å2
Refinement stepCycle: LAST / Resolution: 1.80000915376→24.6308969654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1903 0 59 104 2066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006645067862312055
X-RAY DIFFRACTIONf_angle_d1.189213728012820
X-RAY DIFFRACTIONf_chiral_restr0.0568494568916297
X-RAY DIFFRACTIONf_plane_restr0.00603164044155382
X-RAY DIFFRACTIONf_dihedral_angle_d19.61982094651203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8000092-1.88190.2800228566521680.2726212763632920X-RAY DIFFRACTION99.5165968418
1.8819-1.98110.3293581950871240.2475173550272922X-RAY DIFFRACTION99.3152918161
1.9811-2.10510.2551365615511430.2195387867012932X-RAY DIFFRACTION99.2575855391
2.1051-2.26760.3002200545881460.2062360571112966X-RAY DIFFRACTION99.8395893487
2.2676-2.49560.2535530300581410.2094839297662950X-RAY DIFFRACTION99.8707592892
2.4956-2.85620.2515601339621490.2164926774462968X-RAY DIFFRACTION99.8078770413
2.8562-3.59670.23625961021520.1839540028582969X-RAY DIFFRACTION99.8081228014
3.5967-24.6308969650.1685232446821580.151535848243026X-RAY DIFFRACTION99.6245306633

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