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- PDB-9nsr: Crystal structure of bifunctional farnesyl/geranylgeranyl pyropho... -

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Basic information

Entry
Database: PDB / ID: 9nsr
TitleCrystal structure of bifunctional farnesyl/geranylgeranyl pyrophosphate synthase (FPPS/GGPPS) from Plasmodium falciparum in complex with MMV019313
ComponentsBifunctional farnesyl/geranylgeranyl diphosphate synthase
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / geranylgeranyl pyrophosphate synthase
Function / homology
Function and homology information


Cholesterol biosynthesis / geranylgeranyl diphosphate synthase / geranylgeranyl diphosphate synthase activity / isoprenoid biosynthetic process / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / cytoplasm
Similarity search - Function
Farnesyl pyrophosphate synthase-like / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
: / Bifunctional farnesyl/geranylgeranyl diphosphate synthase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of bifunctional farnesyl/geranylgeranyl pyrophosphate synthase (FPPS/GGPPS) from Plasmodium falciparum in complex with MMV019313
Authors: Lovell, S. / Cooper, A. / Liu, L. / Battaile, K.P.
History
DepositionMar 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional farnesyl/geranylgeranyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0662
Polymers44,6691
Non-polymers3981
Water00
1
A: Bifunctional farnesyl/geranylgeranyl diphosphate synthase
hetero molecules

A: Bifunctional farnesyl/geranylgeranyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1334
Polymers89,3382
Non-polymers7952
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area6620 Å2
ΔGint-40 kcal/mol
Surface area27970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.689, 70.689, 203.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Bifunctional farnesyl/geranylgeranyl diphosphate synthase


Mass: 44668.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF3D7_1128400 / Plasmid: PlfaA.01374.a.BC1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8II79, geranylgeranyl diphosphate synthase
#2: Chemical ChemComp-A1B0W / N-[3-(azepan-1-yl)propyl]-5-methyl-4-oxo-4,5-dihydrothieno[3,2-c]quinoline-2-carboxamide


Mass: 397.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H27N3O2S
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: 2.85 Å3/Da / Density % sol: 56.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Grid Salt HT D2: 1.5 M Sodium malonate pH 6.0. PlfaA.01374.a.BC1.PS38722 at 25 mg/mL. His tag cleaved with 3C protease. 2mM MMV019313 added prior to crystallization, plate 13887 well D2 drop ...Details: Grid Salt HT D2: 1.5 M Sodium malonate pH 6.0. PlfaA.01374.a.BC1.PS38722 at 25 mg/mL. His tag cleaved with 3C protease. 2mM MMV019313 added prior to crystallization, plate 13887 well D2 drop 2, Puck: PSL2016, Cryo: 2.5M sodium malonate pH 6.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Mar 24, 2024
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 3.24→50 Å / Num. obs: 8801 / % possible obs: 99.9 % / Redundancy: 16.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.241 / Rpim(I) all: 0.06 / Rrim(I) all: 0.249 / Χ2: 1.05 / Net I/σ(I): 10.1
Reflection shellResolution: 3.25→3.51 Å / Redundancy: 17.4 % / Rmerge(I) obs: 1.961 / Num. unique obs: 1759 / CC1/2: 0.748 / Rpim(I) all: 0.48 / Rrim(I) all: 2.02 / Χ2: 1.09

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Processing

Software
NameVersionClassification
PHENIX(dev_5533: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.25→44.88 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2947 448 5.11 %
Rwork0.2511 --
obs0.2533 8760 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.25→44.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2797 0 28 0 2825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022884
X-RAY DIFFRACTIONf_angle_d0.4413894
X-RAY DIFFRACTIONf_dihedral_angle_d13.1651063
X-RAY DIFFRACTIONf_chiral_restr0.037427
X-RAY DIFFRACTIONf_plane_restr0.004482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.720.34051510.28582690X-RAY DIFFRACTION100
3.72-4.690.28861360.25572731X-RAY DIFFRACTION100
4.69-44.880.28361610.23832891X-RAY DIFFRACTION100
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)
12.93871.37860.33715.38832.12443.2806-0.20070.5941-0.9327-0.155-0.0106-0.30280.61660.17180.07260.72280.03480.02280.4248-0.12260.889114.2363-45.045736.5478
25.0503-0.24851.54164.6189-2.41977.5498-0.43750.8764-0.2646-0.5097-0.065-0.50760.16430.17120.46710.7112-0.02810.03940.5655-0.12610.89519.9771-38.734530.2609
33.6956-1.36651.24163.42540.19712.93810.16430.59120.5161-0.39180.20110.4685-0.3421-0.0751-0.08830.8046-0.0362-0.02020.41490.07980.86653.4028-20.422929.9285
44.43360.56232.47039.40790.14014.2851-0.36810.6021-0.14130.09970.24950.4081-0.457-0.44560.08410.7859-0.0289-0.00740.4298-0.0060.900716.0144-21.537538.8677
52.8478-1.10931.52210.5577-0.36074.6649-0.51421.81730.6632-0.6432-0.06750.0319-0.4051.55550.42481.192-0.33930.17611.27830.22081.039716.0379-12.671511.2364
63.4719-0.5561-0.52986.948-2.49622.19290.15460.05410.36170.8908-0.2587-1.08250.51020.90050.28460.8802-0.15950.0080.8656-0.10861.49326.3039-16.316638.0846
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 35 through 101 )
2X-RAY DIFFRACTION2chain 'A' and (resid 102 through 171 )
3X-RAY DIFFRACTION3chain 'A' and (resid 172 through 243 )
4X-RAY DIFFRACTION4chain 'A' and (resid 244 through 292 )
5X-RAY DIFFRACTION5chain 'A' and (resid 293 through 356 )
6X-RAY DIFFRACTION6chain 'A' and (resid 357 through 392 )

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