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- PDB-9sm1: FPP-Methyltransferase from Pseudomonas chlororaphis in complex wi... -

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Basic information

Entry
Database: PDB / ID: 9sm1
TitleFPP-Methyltransferase from Pseudomonas chlororaphis in complex with SAH and FPP
ComponentsMethyltransferase domain 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
: / Methyltransferase domain 25 / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
FARNESYL DIPHOSPHATE / PHOSPHATE ION / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase domain protein
Similarity search - Component
Biological speciesPseudomonas chlororaphis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 protein
B: Methyltransferase domain protein
C: Methyltransferase domain protein
D: Methyltransferase domain protein
E: Methyltransferase domain protein
F: Methyltransferase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,21439
Polymers205,2646
Non-polymers5,94933
Water8,521473
1
A: Methyltransferase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,57210
Polymers34,2111
Non-polymers1,3619
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methyltransferase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3577
Polymers34,2111
Non-polymers1,1476
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Methyltransferase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5479
Polymers34,2111
Non-polymers1,3378
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Methyltransferase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2626
Polymers34,2111
Non-polymers1,0525
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Methyltransferase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6903
Polymers34,2111
Non-polymers4792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Methyltransferase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7854
Polymers34,2111
Non-polymers5743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)261.430, 100.040, 89.540
Angle α, β, γ (deg.)90.00, 98.03, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-572-

HOH

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Methyltransferase domain protein


Mass: 34210.730 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas chlororaphis (bacteria) / Gene: PchlO6_6045 / Plasmid: pETDUet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AB33WVX4

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Non-polymers , 5 types, 506 molecules

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


Mass: 384.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FPP / FARNESYL DIPHOSPHATE


Mass: 382.326 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H28O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical...
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 2.82 Å3/Da / Density % sol: 56.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 1.4 M Na/K-Phosphate

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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: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 111920 / % possible obs: 96.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 11.1
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.738 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 13727 / % possible all: 95.3

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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: 2.2→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 13.823 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21739 5594 5 %RANDOM
Rwork0.18429 ---
obs0.18595 106293 96.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.083 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å2-0 Å21.52 Å2
2---0.71 Å20 Å2
3---0.21 Å2
Refinement stepCycle: 1 / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14164 0 363 473 15000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01314899
X-RAY DIFFRACTIONr_bond_other_d0.0010.01513754
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.65520244
X-RAY DIFFRACTIONr_angle_other_deg1.0911.58531624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35651744
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.39520.558914
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.778152392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.53615152
X-RAY DIFFRACTIONr_chiral_restr0.0470.21821
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216798
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023576
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_it1.6183.9717027
X-RAY DIFFRACTIONr_mcbond_other1.6183.9717027
X-RAY DIFFRACTIONr_mcangle_it2.3155.958754
X-RAY DIFFRACTIONr_mcangle_other2.3155.958755
X-RAY DIFFRACTIONr_scbond_it1.5894.227872
X-RAY DIFFRACTIONr_scbond_other1.5414.197784
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1656.20511359
X-RAY DIFFRACTIONr_long_range_B_refined3.88573.92262073
X-RAY DIFFRACTIONr_long_range_B_other3.83973.95761780
X-RAY DIFFRACTIONr_rigid_bond_restr0.437328653
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 400 -
Rwork0.352 7600 -
obs--94.1 %
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)
10.39910.0919-0.1030.4406-0.20730.38660.0058-0.01330.01660.0352-0.0073-0.0184-0.02550.01430.00160.01640.00240.00320.0513-0.00410.014870.30670.83312.6667
20.62440.1353-0.21040.4673-0.09160.53990.0285-0.04480.00480.0533-0.01470.0412-0.012-0.0191-0.01380.0203-0.00080.01110.04790.00060.00743.6197-18.78829.2575
30.35890.0259-0.05310.28410.0310.48060.01140.02850.0403-0.0233-0.004-0.0101-0.0540.0197-0.00740.02510.00020.01240.05160.00650.0184105.1835-10.51744.2768
40.35260.0495-0.11230.4015-0.20380.6647-0.0018-0.03150.0130.0189-0.0023-0.0074-0.03680.0270.00410.01370.00150.00810.0478-0.00390.011100.5715-20.2718-6.8422
50.6318-0.1609-0.06220.3951-0.05190.3513-0.0145-0.0279-0.03870.00870.01230.02170.0219-0.01420.00220.0139-0.00390.00840.05470.00490.010789.2295-45.916231.4204
61.1478-0.0428-0.21320.3277-0.09090.7399-0.0376-0.0864-0.1062-0.01830.0363-0.05570.04910.16350.00130.02490.03570.01470.0925-0.00730.0415129.6448-53.718919.1364
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 502
2X-RAY DIFFRACTION2B24 - 501
3X-RAY DIFFRACTION3C24 - 501
4X-RAY DIFFRACTION4D24 - 501
5X-RAY DIFFRACTION5E24 - 401
6X-RAY DIFFRACTION6F24 - 401

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