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- PDB-24uw: Crystal structure of FPP-methyltransferase VbFPPMT from Variovora... -

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Basic information

Entry
Database: PDB / ID: 24uw
TitleCrystal structure of FPP-methyltransferase VbFPPMT from Variovorax boronicumulans PHE5-4 in complex with SAH
ComponentsFPP-methyltransferase VbFPPMT
KeywordsTRANSFERASE / FPP / SAH / methyltransferase
Function / homology2,3-DIHYDROXY-1,4-DITHIOBUTANE / S-ADENOSYL-L-HOMOCYSTEINE
Function and homology information
Biological speciesVariovorax boronicumulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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 VbFPPMT from Variovorax boronicumulans PHE5-4 in complex with SAH
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

Downloads & links

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Assembly

Deposited unit
A: FPP-methyltransferase VbFPPMT
B: FPP-methyltransferase VbFPPMT
C: FPP-methyltransferase VbFPPMT
D: FPP-methyltransferase VbFPPMT
E: FPP-methyltransferase VbFPPMT
F: FPP-methyltransferase VbFPPMT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,10814
Polymers211,4936
Non-polymers2,6158
Water27,8331545
1
A: FPP-methyltransferase VbFPPMT
hetero molecules

F: FPP-methyltransferase VbFPPMT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5756
Polymers70,4982
Non-polymers1,0774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1/2,-y,z-1/21
Buried area2480 Å2
ΔGint-17 kcal/mol
Surface area23210 Å2
MethodPISA
2
B: FPP-methyltransferase VbFPPMT
E: FPP-methyltransferase VbFPPMT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2674
Polymers70,4982
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-8 kcal/mol
Surface area23190 Å2
MethodPISA
3
C: FPP-methyltransferase VbFPPMT
D: FPP-methyltransferase VbFPPMT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2674
Polymers70,4982
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-11 kcal/mol
Surface area23670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.885, 131.748, 168.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
FPP-methyltransferase VbFPPMT


Mass: 35248.887 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Variovorax boronicumulans (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#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-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1545 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 20% PEG 6000, 1.0 M LiCl, 0.1 M Tris, pH 8.0

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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: Dec 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.76→25 Å / Num. obs: 180663 / % possible obs: 98.7 % / Redundancy: 4.7 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.03 / Rrim(I) all: 0.068 / Χ2: 0.892 / Net I/σ(I): 9.3 / Num. measured all: 849344
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.76-1.824.40.553177560.9110.9760.2840.6240.44697.8
1.82-1.94.50.412177830.9420.9850.2110.4650.47298
1.9-1.984.50.281178130.9720.9930.1440.3160.52198.4
1.98-2.094.60.2179240.9820.9960.1020.2250.58298.5
2.09-2.224.70.142179010.9890.9970.0720.1590.7198.6
2.22-2.394.90.11181000.9920.9980.0550.1240.87999.2
2.39-2.634.90.088181330.9940.9980.0440.0991.15799.3
2.63-3.014.90.07182450.9950.9990.0350.0791.29499.5
3.01-3.7950.053182160.9970.9990.0260.061.33598.8
3.79-254.60.041187920.9980.9990.020.0461.33999

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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: 1.76→24.86 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2325 9213 5.1 %
Rwork0.184 --
obs0.1865 180528 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.76→24.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14126 0 172 1545 15843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714722
X-RAY DIFFRACTIONf_angle_d0.93420024
X-RAY DIFFRACTIONf_dihedral_angle_d15.2045674
X-RAY DIFFRACTIONf_chiral_restr0.0582161
X-RAY DIFFRACTIONf_plane_restr0.0092670
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.780.29782780.25275064X-RAY DIFFRACTION88
1.78-1.80.30453040.25585586X-RAY DIFFRACTION98
1.8-1.830.32353080.24595651X-RAY DIFFRACTION98
1.83-1.850.28993090.23645618X-RAY DIFFRACTION98
1.85-1.870.27452930.22915634X-RAY DIFFRACTION98
1.87-1.90.29153450.22875596X-RAY DIFFRACTION98
1.9-1.930.30863000.22825670X-RAY DIFFRACTION98
1.93-1.960.26693170.21025635X-RAY DIFFRACTION98
1.96-1.990.27382910.20855680X-RAY DIFFRACTION99
1.99-2.020.26843120.21775672X-RAY DIFFRACTION99
2.02-2.050.26713330.21045662X-RAY DIFFRACTION98
2.05-2.090.27242830.21565727X-RAY DIFFRACTION98
2.09-2.130.2712680.21175684X-RAY DIFFRACTION99
2.13-2.170.25762900.20625667X-RAY DIFFRACTION98
2.17-2.220.27143040.20185733X-RAY DIFFRACTION99
2.22-2.270.24243320.20075720X-RAY DIFFRACTION99
2.27-2.330.23563200.20635742X-RAY DIFFRACTION99
2.33-2.390.27693070.20795706X-RAY DIFFRACTION99
2.39-2.460.2633190.20825729X-RAY DIFFRACTION99
2.46-2.540.26263120.20475780X-RAY DIFFRACTION99
2.54-2.630.25062900.20115779X-RAY DIFFRACTION100
2.63-2.740.25623150.20215780X-RAY DIFFRACTION100
2.74-2.860.25212890.19885811X-RAY DIFFRACTION100
2.86-3.010.24942820.20215814X-RAY DIFFRACTION99
3.01-3.20.23293290.18785730X-RAY DIFFRACTION99
3.2-3.450.22613000.17595774X-RAY DIFFRACTION99
3.45-3.80.22673260.16535822X-RAY DIFFRACTION99
3.8-4.340.1723310.14545847X-RAY DIFFRACTION99
4.34-5.460.19113000.14245930X-RAY DIFFRACTION99
5.46-24.860.19473260.16226072X-RAY DIFFRACTION98

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