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- PDB-9sm5: gamma-PSPP-Methyltransferase from Pseudomonas chlororaphis in com... -

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Basic information

Entry
Database: PDB / ID: 9sm5
Titlegamma-PSPP-Methyltransferase from Pseudomonas chlororaphis in complex with SAH and alpha-PSPP
ComponentsMethyltransferase domain protein
KeywordsBIOSYNTHETIC PROTEIN / Terpene Biosynthesis / SAM-dependent C-methyltransferases / Methylation-triggered cyclization / Carbocation cascades / Structural enzymology
Function / homology: / Methyltransferase domain / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / : / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase domain protein
Function and homology information
Biological speciesPseudomonas chlororaphis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,0619
Polymers104,3193
Non-polymers1,7426
Water1,11762
1
A: Methyltransferase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5543
Polymers34,7731
Non-polymers7812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methyltransferase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2533
Polymers34,7731
Non-polymers4802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Methyltransferase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2533
Polymers34,7731
Non-polymers4802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.450, 83.670, 121.740
Angle α, β, γ (deg.)90.00, 90.64, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Methyltransferase domain protein


Mass: 34772.969 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas chlororaphis (bacteria) / Gene: PchlO6_6042 / Plasmid: pETDUet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AB33WUZ9
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1JOQ / alpha-presodorifen diphosphate / [(~{E})-3-methyl-5-[(1~{S},4~{R},5~{R})-1,2,3,4,5-pentamethylcyclopent-2-en-1-yl]pent-2-enyl] phosphono hydrogen phosphate


Mass: 396.353 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H30O7P2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.6 Å3/Da / Density % sol: 52.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M TRIS, 0.2 M MgCl2, 20% PEG 8000

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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: Nov 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 32260 / % possible obs: 97.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 7.5
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 2 / Num. unique obs: 3508 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.911 / SU B: 26.819 / SU ML: 0.259 / Cross valid method: THROUGHOUT / ESU R: 0.725 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24224 1612 5 %RANDOM
Rwork0.20545 ---
obs0.20943 30634 97.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.676 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0 Å2-1.05 Å2
2---1.19 Å20 Å2
3---1.56 Å2
Refinement stepCycle: 1 / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6495 0 113 62 6670
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0136763
X-RAY DIFFRACTIONr_bond_other_d0.0020.0156246
X-RAY DIFFRACTIONr_angle_refined_deg1.321.6559164
X-RAY DIFFRACTIONr_angle_other_deg1.111.59214359
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4595796
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.28520.724428
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.607151115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1871574
X-RAY DIFFRACTIONr_chiral_restr0.050.2840
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027704
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021681
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_it1.0243.7243211
X-RAY DIFFRACTIONr_mcbond_other1.0243.7243211
X-RAY DIFFRACTIONr_mcangle_it1.8155.5823998
X-RAY DIFFRACTIONr_mcangle_other1.8145.5823999
X-RAY DIFFRACTIONr_scbond_it0.8593.8493552
X-RAY DIFFRACTIONr_scbond_other0.8433.8413548
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.535.7155161
X-RAY DIFFRACTIONr_long_range_B_refined4.10941.9567274
X-RAY DIFFRACTIONr_long_range_B_other4.09741.9437267
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 119 -
Rwork0.336 2275 -
obs--99.54 %
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)
11.80430.74980.24861.8577-0.170.1691-0.1020.0748-0.0302-0.00370.0851-0.1194-0.0159-0.05840.01690.3685-0.0019-0.03340.2041-0.01740.317918.5592-0.838457.6133
21.3672-0.02230.14841.23150.12641.0453-0.00970.116-0.0322-0.10990.05380.03780.2063-0.1227-0.0440.443-0.1819-0.04210.4685-0.06060.021517.52946.967117.1945
30.80660.12980.34571.8439-0.10971.1254-0.26840.1631-0.015-0.00990.0369-0.0407-0.2761-0.10140.23150.3865-0.0485-0.11970.45120.06450.11225.844844.417823.3946
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 402
2X-RAY DIFFRACTION2B17 - 401
3X-RAY DIFFRACTION3C19 - 401

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