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- PDB-24uy: Crystal structure of FPP-methyltransferase PcFPPMT from Pseudomon... -

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Basic information

Entry
Database: PDB / ID: 24uy
TitleCrystal structure of FPP-methyltransferase PcFPPMT from Pseudomonas chlororaphis O6 in complex with SAH and GPP
ComponentsMethyltransferase domain protein
KeywordsTRANSFERASE / FPP / SAH / methyltransferase
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
GERANYL DIPHOSPHATE / IMIDAZOLE / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase domain protein
Similarity search - Component
Biological speciesPseudomonas chlororaphis O6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLi, X.Q. / Huang, J.-W. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of FPP-methyltransferase PcFPPMT from Pseudomonas chlororaphis O6 in complex with SAH and GPP
Authors: Li, X.Q. / Huang, J.-W. / Chen, C.-C. / Guo, R.-T.
History
DepositionMar 22, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyltransferase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8955
Polymers35,1031
Non-polymers7924
Water3,297183
1
A: Methyltransferase domain protein
hetero molecules

A: Methyltransferase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,78910
Polymers70,2052
Non-polymers1,5848
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area3840 Å2
ΔGint-24 kcal/mol
Surface area23130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.686, 98.353, 42.315
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Methyltransferase domain protein


Mass: 35102.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas chlororaphis O6 (bacteria) / Gene: PchlO6_6045 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AB33WVX4

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Non-polymers , 5 types, 187 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-GPP / GERANYL DIPHOSPHATE


Mass: 314.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.12 Å3/Da / Density % sol: 41.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 25% PEG 3350, 0.2 M MgCl2, 0.1 M Imidazole, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 07A / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Oct 26, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 31615 / % possible obs: 98.4 % / Redundancy: 5 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.02 / Rrim(I) all: 0.044 / Χ2: 0.92 / Net I/σ(I): 16.7 / Num. measured all: 158970
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.7-1.7640.47930720.8370.9550.2620.5490.46397
1.76-1.835.20.33231350.9210.9790.1580.3690.51100
1.83-1.915.40.22931410.960.990.1070.2530.57799
1.91-2.025.30.15231600.9850.9960.0710.1680.6999.7
2.02-2.145.40.10531450.990.9980.0490.1160.8799.3
2.14-2.315.30.07331550.9950.9990.0350.0821.13499.2
2.31-2.545.30.05731710.9970.9990.0270.0641.30599
2.54-2.915.10.04731330.9970.9990.0230.0521.31797.5
2.91-3.664.80.03632110.99810.0180.0411.29198.1
3.66-504.50.02832920.99810.0150.0320.95795.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→28.16 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2321 1574 4.99 %
Rwork0.1938 --
obs0.1957 31567 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→28.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2416 0 51 183 2650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082553
X-RAY DIFFRACTIONf_angle_d1.0033469
X-RAY DIFFRACTIONf_dihedral_angle_d13.744984
X-RAY DIFFRACTIONf_chiral_restr0.062362
X-RAY DIFFRACTIONf_plane_restr0.009464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.760.3251360.28662605X-RAY DIFFRACTION95
1.76-1.820.28791600.25732670X-RAY DIFFRACTION100
1.82-1.890.33571240.25232731X-RAY DIFFRACTION99
1.89-1.980.29551810.24642691X-RAY DIFFRACTION100
1.98-2.080.26651320.22812734X-RAY DIFFRACTION99
2.08-2.220.24631310.21662748X-RAY DIFFRACTION100
2.22-2.390.24281340.22142746X-RAY DIFFRACTION99
2.39-2.630.19341490.21562730X-RAY DIFFRACTION99
2.63-3.010.2811420.2052730X-RAY DIFFRACTION97
3.01-3.780.24371260.17872784X-RAY DIFFRACTION98
3.79-28.160.18741590.16092824X-RAY DIFFRACTION96

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