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- PDB-9sls: FPP-Methyltransferase from Burkholderia sp. in complex with SAH -

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Basic information

Entry
Database: PDB / ID: 9sls
TitleFPP-Methyltransferase from Burkholderia sp. in complex with SAH
ComponentsMethyltransferase type 12
KeywordsBIOSYNTHETIC PROTEIN / Terpene Biosynthesis / SAM-dependent C-methyltransferases / Methylation-triggered cyclization / Carbocation cascades / Structural enzymology
Function / homologyS-ADENOSYL-L-HOMOCYSTEINE / :
Function and homology information
Biological speciesBurkholderia sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 type 12
B: Methyltransferase type 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,08420
Polymers69,3232
Non-polymers1,76218
Water4,234235
1
A: Methyltransferase type 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,60411
Polymers34,6611
Non-polymers94310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methyltransferase type 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4809
Polymers34,6611
Non-polymers8198
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.680, 87.680, 173.730
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Methyltransferase type 12


Mass: 34661.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia sp. (bacteria) / Gene: WS68_00570 / Plasmid: pETDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A103EKV8
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.78 Å3/Da / Density % sol: 55.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% Ethylene Glycol

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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: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 68843 / % possible obs: 98.7 % / Redundancy: 3 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 13.4
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 2 / Num. unique obs: 10362 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 6.918 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19189 3442 5 %RANDOM
Rwork0.15608 ---
obs0.15791 65392 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.428 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å2-0.37 Å20 Å2
2---0.75 Å2-0 Å2
3---2.42 Å2
Refinement stepCycle: 1 / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4330 0 116 235 4681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0134566
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154274
X-RAY DIFFRACTIONr_angle_refined_deg1.2991.6566171
X-RAY DIFFRACTIONr_angle_other_deg1.2391.5839827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2445535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.18621.567268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7415748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.941538
X-RAY DIFFRACTIONr_chiral_restr0.0660.2570
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025126
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021084
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_it2.5773.1332140
X-RAY DIFFRACTIONr_mcbond_other2.5763.1332140
X-RAY DIFFRACTIONr_mcangle_it3.3964.7022666
X-RAY DIFFRACTIONr_mcangle_other3.3964.7022667
X-RAY DIFFRACTIONr_scbond_it3.063.6172426
X-RAY DIFFRACTIONr_scbond_other3.0593.6182427
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9525.2443503
X-RAY DIFFRACTIONr_long_range_B_refined4.67437.2665061
X-RAY DIFFRACTIONr_long_range_B_other4.63637.1235034
X-RAY DIFFRACTIONr_rigid_bond_restr1.12238840
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 255 -
Rwork0.337 4846 -
obs--99.61 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.33040.19450.00850.9371-0.02250.00240.1261-0.0428-0.0108-0.0009-0.1290.0266-0.0010.00780.00290.0946-0.0397-0.01540.04580.00390.007-37.6144-1.180.1147
20.61990.44790.09760.45820.19340.2907-0.013-0.04030.04920.0287-0.03320.01190.0565-0.00770.04630.0357-0.01510.00340.0189-0.01510.0568-61.1228-34.349811.6862
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 401
2X-RAY DIFFRACTION2B19 - 401

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