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- PDB-6si5: T. cruzi FPPS in complex with 1-methyl-5-(4,5,6,7-tetrahydrothien... -

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Basic information

Entry
Database: PDB / ID: 6si5
TitleT. cruzi FPPS in complex with 1-methyl-5-(4,5,6,7-tetrahydrothieno[3,2-c]pyridine-5-carbonyl)pyridin-2(1H)-one
ComponentsFarnesyl diphosphate synthase
KeywordsTRANSFERASE / farnesyl diphosphate synthase / sterol biosynthesis / farnesyl pyrophosphate / homodimer
Function / homology
Function and homology information


farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / metal ion binding / membrane / cytoplasm
Similarity search - Function
Farnesyl pyrophosphate synthase-like / Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
Chem-LEQ / Farnesyl diphosphate synthase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.097 Å
AuthorsPetrick, J.K. / Muenzker, L. / Schleberger, C. / Cornaciu, I. / Clavel, D. / Marquez, J.A. / Jahnke, W.
Funding support2items
OrganizationGrant numberCountry
European Commission765555
Accelerated Early staGe drug dIScovery765555
CitationJournal: Thesis / Year: 2019
Title: Targeting farnesyl pyrophosphate synthase of Trypanosoma cruzi by fragment-based lead discovery
Authors: Petrick, J.K. / Jahnke, W.
History
DepositionAug 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8264
Polymers41,3601
Non-polymers4663
Water2,864159
1
A: Farnesyl diphosphate synthase
hetero molecules

A: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6528
Polymers82,7192
Non-polymers9336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area6810 Å2
ΔGint-99 kcal/mol
Surface area28580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.061, 58.061, 396.793
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Farnesyl diphosphate synthase


Mass: 41359.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8WS26
#2: Chemical ChemComp-LEQ / 5-(6,7-dihydro-4~{H}-thieno[3,2-c]pyridin-5-ylcarbonyl)-1-methyl-pyridin-2-one


Mass: 274.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14N2O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.33 Å3/Da / Density % sol: 47.3 % / Mosaicity: 0.08 °
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 80 mM MES: 4.0 mM ZnSO4: 12.36 % PEG MME 550: 11.57% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.097→66.132 Å / Num. obs: 24665 / % possible obs: 99.7 % / Redundancy: 35.9 % / Biso Wilson estimate: 41.68 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.03 / Rrim(I) all: 0.174 / Rsym value: 0.172 / Net I/σ(I): 16.6
Reflection shellResolution: 2.097→2.133 Å / Redundancy: 37.5 % / Rmerge(I) obs: 2.109 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1185 / CC1/2: 0.774 / Rpim(I) all: 0.344 / Rrim(I) all: 2.138 / Rsym value: 2.109 / % possible all: 99.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_TRA
Highest resolutionLowest resolution
Translation3 Å66.13 Å

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Processing

Software
NameVersionClassification
BUSTERrefinement
Aimless0.5.32data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
XDS20180126data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DWG

4dwg


Resolution: 2.097→66.132 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.932 / SU R Cruickshank DPI: 0.204 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.228 / SU Rfree Blow DPI: 0.199 / SU Rfree Cruickshank DPI: 0.19
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1233 5 %RANDOM
Rwork0.2 ---
obs0.203 24665 99.7 %-
Displacement parametersBiso max: 127.48 Å2 / Biso mean: 46.64 Å2 / Biso min: 24.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.1968 Å20 Å20 Å2
2---3.1968 Å20 Å2
3---6.3937 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: final / Resolution: 2.097→66.132 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2788 0 29 159 2976
Biso mean--68.86 53.14 -
Num. residues----354
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d975SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes493HARMONIC5
X-RAY DIFFRACTIONt_it2904HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion375SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3670SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2904HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3951HARMONIC20.92
X-RAY DIFFRACTIONt_omega_torsion2.72
X-RAY DIFFRACTIONt_other_torsion16.59
LS refinement shellResolution: 2.1→2.11 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2094 29 5.87 %
Rwork0.2055 465 -
all0.2058 494 -
obs--99.17 %
Refinement TLS params.Method: refined / Origin x: -9.2169 Å / Origin y: -17.4429 Å / Origin z: -20.327 Å
111213212223313233
T-0.0711 Å20.0159 Å2-0.0017 Å2--0.0404 Å2-0.0204 Å2---0.0492 Å2
L1.4134 °2-0.0436 °2-0.1579 °2-0.4919 °2-0.0737 °2--0.5216 °2
S-0.0365 Å °-0.238 Å °0.1767 Å °0.0833 Å °0.0229 Å °-0.0197 Å °-0.0455 Å °0.0575 Å °0.0136 Å °
Refinement TLS groupSelection details: { A|* }

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