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- PDB-9khp: The crystal structure of XhnM1 with SAH -

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Basic information

Entry
Database: PDB / ID: 9khp
TitleThe crystal structure of XhnM1 with SAH
ComponentsClass I SAM-dependent methyltransferase
KeywordsTRANSFERASE / methyl group / Xinhaicarxin BG
Function / homologyMethyltransferase domain 25 / Methyltransferase domain / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / ACETATE ION / CYSTEINE / S-ADENOSYL-L-HOMOCYSTEINE / Class I SAM-dependent methyltransferase
Function and homology information
Biological speciesStreptomyces xinghaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73006100024 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 11, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5407
Polymers29,7731
Non-polymers7676
Water3,657203
1
A: Class I SAM-dependent methyltransferase
hetero molecules

A: Class I SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,08114
Polymers59,5472
Non-polymers1,53412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+3/21
Buried area3640 Å2
ΔGint-19 kcal/mol
Surface area21700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.990, 124.320, 69.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Class I SAM-dependent methyltransferase


Mass: 29773.377 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 (E. coli) / References: UniProt: A0A3R7FZU3

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Non-polymers , 6 types, 209 molecules

#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Feature type: SUBJECT OF INVESTIGATION / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M imidazole hydrochloride acid pH 8.0,0.2 M calcium acetate, and 10% pEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.73→46.450163 Å / Num. obs: 27619 / % possible obs: 98.4 % / Redundancy: 13.3 % / Biso Wilson estimate: 23.8497643409 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Net I/σ(I): 17.8
Reflection shellResolution: 1.74→1.83 Å / Rmerge(I) obs: 0.94 / Num. unique obs: 3887 / CC1/2: 0.878

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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: 1.73006100024→46.4501629927 Å / SU ML: 0.145262600305 / Cross valid method: FREE R-VALUE / σ(F): 1.34362631118 / Phase error: 19.2753525329
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.203326918856 1347 4.87760718424 %
Rwork0.177775340518 26269 -
obs0.179048283691 27616 98.1518339494 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.5872662042 Å2
Refinement stepCycle: LAST / Resolution: 1.73006100024→46.4501629927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1933 0 49 203 2185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006327398103522023
X-RAY DIFFRACTIONf_angle_d0.9173667198872750
X-RAY DIFFRACTIONf_chiral_restr0.0544578733308294
X-RAY DIFFRACTIONf_plane_restr0.00587783715403374
X-RAY DIFFRACTIONf_dihedral_angle_d20.20975120491189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7301-1.79190.2685308841151220.2353228958992568X-RAY DIFFRACTION96.9369369369
1.7919-1.86360.2472928265481350.2156673316712548X-RAY DIFFRACTION97.528171574
1.8636-1.94850.2342678816421370.1983287291642573X-RAY DIFFRACTION97.4119338605
1.9485-2.05120.2163343294391450.1816715090912591X-RAY DIFFRACTION97.7491961415
2.0512-2.17970.2082443859991300.168006618962607X-RAY DIFFRACTION97.8198713367
2.1797-2.3480.2056825806981370.1700936866462611X-RAY DIFFRACTION98.2130092924
2.348-2.58430.2371665466131320.1834911816152622X-RAY DIFFRACTION98.3220278472
2.5843-2.95820.207232251761240.1839993700132647X-RAY DIFFRACTION98.9996427295
2.9582-3.72670.180071344111330.1663518179222701X-RAY DIFFRACTION99.194959748
3.7267-46.450162990.179417808071520.1674873522422801X-RAY DIFFRACTION99.2605042017

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