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- PDB-9sm0: FPP-Methyltransferase from Burkholderia territorii in complex with SAH -

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Basic information

Entry
Database: PDB / ID: 9sm0
TitleFPP-Methyltransferase from Burkholderia territorii in complex with SAH
ComponentsMethyltransferase domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / Terpene Biosynthesis / SAM-dependent C-methyltransferases / Methylation-triggered cyclization / Carbocation cascades / Structural enzymology
Function / homology
Function and homology information


methyltransferase activity / methylation
Similarity search - Function
Polyketide synthase, methyltransferase domain / Methyltransferase in polyketide synthase (PKS) enzymes. / : / Methyltransferase domain 25 / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
CARBONATE ION / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase domain-containing protein
Similarity search - Component
Biological speciesBurkholderia territorii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsGroll, M. / Yang, K. / Xu, H. / Troycke, P. / Dickschat, J.S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)GR 1861/13-1 Germany
CitationJournal: to be published
Title: Structural basis of methylation-triggered cyclization
Authors: Groll, M. / Yang, K. / Xu, H. / Troycke, P. / Dickschat, J.S.
History
DepositionSep 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 31, 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: Methyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,79213
Polymers33,5111
Non-polymers1,28112
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-78 kcal/mol
Surface area13210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.630, 108.630, 73.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Methyltransferase domain-containing protein


Mass: 33510.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia territorii (bacteria) / Gene: F7R13_03825 / Plasmid: pETDUet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6L3NMB0

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Non-polymers , 6 types, 322 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-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 3.23 Å3/Da / Density % sol: 61.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES, 25% PEG 3350, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0597 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 13, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0597 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 85663 / % possible obs: 99 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.6
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.781 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 15903 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→30 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.63 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1683 4280 5 %RANDOM
Rwork0.14537 ---
obs0.14651 81328 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.905 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.06 Å2
Refinement stepCycle: 1 / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2208 0 74 312 2594
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132357
X-RAY DIFFRACTIONr_bond_other_d0.0020.0152163
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.6483210
X-RAY DIFFRACTIONr_angle_other_deg1.3861.5854976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0785278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.69721.095137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90915376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7791521
X-RAY DIFFRACTIONr_chiral_restr0.0750.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022638
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02555
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7591.9391103
X-RAY DIFFRACTIONr_mcbond_other1.7591.9391103
X-RAY DIFFRACTIONr_mcangle_it2.3262.9121375
X-RAY DIFFRACTIONr_mcangle_other2.3262.9121376
X-RAY DIFFRACTIONr_scbond_it2.7032.4591254
X-RAY DIFFRACTIONr_scbond_other2.3732.3291221
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0413.3611785
X-RAY DIFFRACTIONr_long_range_B_refined4.13925.8812774
X-RAY DIFFRACTIONr_long_range_B_other3.65124.9012685
X-RAY DIFFRACTIONr_rigid_bond_restr1.32234519
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 316 -
Rwork0.277 5998 -
obs--99.84 %

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