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- PDB-9sm3: gamma-PSPP-Methyltransferase from Pseudomonas chlororaphis in com... -

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Basic information

Entry
Database: PDB / ID: 9sm3
Titlegamma-PSPP-Methyltransferase from Pseudomonas chlororaphis in complex with SAH
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: 2.05 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)211,25516
Polymers208,6386
Non-polymers2,61810
Water6,179343
1
A: Methyltransferase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1572
Polymers34,7731
Non-polymers3841
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)35,1572
Polymers34,7731
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Methyltransferase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2764
Polymers34,7731
Non-polymers5033
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: 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
6
F: Methyltransferase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1572
Polymers34,7731
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.220, 68.320, 120.680
Angle α, β, γ (deg.)89.88, 89.52, 76.31
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Methyltransferase domain protein


Mass: 34772.969 Da / Num. of mol.: 6
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.: 6 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.62 Å3/Da / Density % sol: 53.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M BIS-TRIS, 1.5 M (NH4)2SO4

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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: 2.05→30 Å / Num. obs: 124759 / % possible obs: 93.9 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 8.4
Reflection shellResolution: 2.05→2.15 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.727 / Mean I/σ(I) obs: 2 / Num. unique obs: 16943 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 12.806 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21431 6236 5 %RANDOM
Rwork0.17788 ---
obs0.17986 118495 93.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.533 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å20.06 Å20.99 Å2
2---0.58 Å2-1 Å2
3---2.49 Å2
Refinement stepCycle: 1 / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13624 0 172 343 14139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01314156
X-RAY DIFFRACTIONr_bond_other_d0.0010.01513017
X-RAY DIFFRACTIONr_angle_refined_deg1.221.64819179
X-RAY DIFFRACTIONr_angle_other_deg1.1351.58429937
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.56551681
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.0520.8888
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62152326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.78615150
X-RAY DIFFRACTIONr_chiral_restr0.0510.21768
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216173
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023501
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_it1.9463.4186778
X-RAY DIFFRACTIONr_mcbond_other1.9463.4186778
X-RAY DIFFRACTIONr_mcangle_it2.765.1248441
X-RAY DIFFRACTIONr_mcangle_other2.765.1238442
X-RAY DIFFRACTIONr_scbond_it1.9563.7117378
X-RAY DIFFRACTIONr_scbond_other1.9493.7077366
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6565.45310721
X-RAY DIFFRACTIONr_long_range_B_refined3.84139.24515553
X-RAY DIFFRACTIONr_long_range_B_other3.82539.21415523
X-RAY DIFFRACTIONr_rigid_bond_restr0.615327173
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 470 -
Rwork0.301 8942 -
obs--96.09 %
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)
10.0448-0.0108-0.0110.11350.01980.0332-0.0029-0.0025-0.00070.00070.00230.0003-0.00170.00130.00070.06010.0091-0.00520.04320.01140.004-12.9383-12.883457.8872
20.108-0.02470.00360.0458-0.0160.0340.0017-0.00160.004-0.002-0.0019-0.00160.00110.00050.00020.0610.0089-0.00510.0420.01030.003617.202210.696963.29
30.0690.0191-0.0190.0721-0.01030.0398-0.00380.0017-0.0015-0.00510.0011-0.00170.00230.0010.00270.06160.0097-0.00390.04250.01050.003524.698912.995423.1576
40.0948-0.00030.00160.08060.01670.0685-0.00080.0002-0.0034-0.00290.00010.0025-0.0022-0.00160.00070.06160.0088-0.00370.04270.01090.0036-7.8063-18.475817.9738
50.07150.01070.01070.07790.00960.0452-0.0002-0.0049-0.0044-0.0009-0.0004-0.0005-0.0009-0.0020.00060.0610.0097-0.00370.04520.01080.003420.06683.7304-17.7436
60.09470.0017-0.02510.0611-0.00830.0494-0.0021-0.0056-0.0075-0.0003-0.00110.00020.0014-0.00030.00320.06080.0102-0.0050.04330.01130.0044-18.2011-20.3683-23.0017
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 401
2X-RAY DIFFRACTION2B17 - 401
3X-RAY DIFFRACTION3C17 - 401
4X-RAY DIFFRACTION4D6 - 401
5X-RAY DIFFRACTION5E6 - 401
6X-RAY DIFFRACTION6F17 - 401

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