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- PDB-6shv: T. cruzi FPPS in complex with 5-(4-fluorophenoxy)pyridin-2-amine -

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Basic information

Entry
Database: PDB / ID: 6shv
TitleT. cruzi FPPS in complex with 5-(4-fluorophenoxy)pyridin-2-amine
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
5-(4-fluoranylphenoxy)pyridin-2-amine / Farnesyl diphosphate synthase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.808 Å
AuthorsPetrick, J.K. / Muenzker, L. / Schleberger, C. / Cornaciu, I. / Clavel, D. / Marquez, J.A. / Jahnke, W.
Funding support1items
OrganizationGrant numberCountry
European Commission765555
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)41,9295
Polymers41,3601
Non-polymers5704
Water3,711206
1
A: Farnesyl diphosphate synthase
hetero molecules

A: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,85910
Polymers82,7192
Non-polymers1,1408
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area6660 Å2
ΔGint-149 kcal/mol
Surface area28170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.213, 58.213, 398.308
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-LDW / 5-(4-fluoranylphenoxy)pyridin-2-amine


Mass: 204.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H9FN2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.36 Å3/Da / Density % sol: 47.78 % / Mosaicity: 0.05 °
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 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.808→44.978 Å / Num. obs: 38338 / % possible obs: 100 % / Redundancy: 12.3 % / Biso Wilson estimate: 27.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.03 / Rrim(I) all: 0.103 / Rsym value: 0.099 / Net I/σ(I): 15.1
Reflection shellResolution: 1.808→1.839 Å / Redundancy: 12.2 % / Rmerge(I) obs: 1.223 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1850 / CC1/2: 0.705 / Rpim(I) all: 0.361 / Rrim(I) all: 1.277 / Rsym value: 1.223 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_TRA
Highest resolutionLowest resolution
Translation3 Å47.13 Å

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Processing

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

4dwg


Resolution: 1.808→44.978 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU R Cruickshank DPI: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.109 / SU Rfree Blow DPI: 0.107 / SU Rfree Cruickshank DPI: 0.103
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 2234 5.02 %RANDOM
Rwork0.1956 ---
obs0.197 38338 89.3 %-
Displacement parametersBiso max: 103.34 Å2 / Biso mean: 34.05 Å2 / Biso min: 15.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.1802 Å20 Å20 Å2
2--0.1802 Å20 Å2
3----0.3604 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: final / Resolution: 1.808→44.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2763 0 36 206 3005
Biso mean--37.64 43.35 -
Num. residues----351
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d977SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes492HARMONIC5
X-RAY DIFFRACTIONt_it2904HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion374SEMIHARMONIC5
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_contact3751SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2904HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3950HARMONIC20.87
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion15.48
LS refinement shellResolution: 1.808→1.839 Å / Rfactor Rfree error: 0
Num. reflection% reflection
Rfree57 6.4 %
Rwork1850 -
obs-100 %
Refinement TLS params.Method: refined / Origin x: -9.2047 Å / Origin y: -17.8696 Å / Origin z: -20.6741 Å
111213212223313233
T-0.0756 Å20.0374 Å2-0.0046 Å2--0.0105 Å2-0.0199 Å2---0.0511 Å2
L1.2031 °2-0.0339 °2-0.1656 °2-0.4101 °20.0074 °2--0.4192 °2
S-0.0292 Å °-0.2277 Å °0.1483 Å °0.0619 Å °0.0052 Å °-0.0369 Å °-0.0291 Å °0.0495 Å °0.024 Å °
Refinement TLS groupSelection details: { A|* }

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