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- PDB-6r09: T. cruzi FPPS in complex with 2-(4-((1H-indol-3-yl)methyl)piperaz... -

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Basic information

Entry
Database: PDB / ID: 6r09
TitleT. cruzi FPPS in complex with 2-(4-((1H-indol-3-yl)methyl)piperazin-1-yl)benzo[d]thiazole
ComponentsFarnesyl diphosphate synthase
KeywordsTRANSFERASE / farnesyl diphosphate synthase / sterol biosynthesis / farnesyl pyrophosphate / homodimer
Function / homology
Function and homology information


farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / membrane / metal ion binding / cytoplasm
Similarity search - Function
Farnesyl pyrophosphate synthase-like / Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-JMK / Farnesyl diphosphate synthase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.28 Å
AuthorsPetrick, J.K. / Muenzker, L. / Schleberger, C. / Jahnke, W.
Funding support1items
OrganizationGrant numberCountry
Accelerated Early staGe drug dIScovery (AEGIS)765555
CitationJournal: Thesis / Year: 2019
Title: Targeting farnesyl pyrophosphate synthase of Trypanosoma cruzi by fragment-based lead discovery
Authors: Petrick, J.K. / Jahnke, W.
History
DepositionMar 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 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)42,0316
Polymers41,3601
Non-polymers6715
Water4,756264
1
A: Farnesyl diphosphate synthase
hetero molecules

A: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,06212
Polymers82,7192
Non-polymers1,34310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area7200 Å2
ΔGint-224 kcal/mol
Surface area28730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.105, 58.105, 397.072
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
Details: termini not resolved / Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8WS26
#2: Chemical ChemComp-JMK / 2-[4-(1~{H}-indol-3-ylmethyl)piperazin-1-yl]-1,3-benzothiazole


Mass: 348.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20N4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.42 % / Mosaicity: 0.03 °
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 80 mM MES: 4 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: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.278→66.179 Å / Num. obs: 96670 / % possible obs: 92.3 % / Redundancy: 18.6 % / Biso Wilson estimate: 20.87 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.025 / Rrim(I) all: 0.106 / Rsym value: 0.103 / Net I/σ(I): 11.7
Reflection shellResolution: 1.278→1.3 Å / Redundancy: 18.6 % / Rmerge(I) obs: 4.077 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 5120 / CC1/2: 0.462 / Rpim(I) all: 0.96 / Rrim(I) all: 4.191 / Rsym value: 4.077 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_TRA
Highest resolutionLowest resolution
Translation3 Å66.18 Å

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Processing

Software
NameVersionClassification
XDS20180126data reduction
Aimless0.7.2data scaling
PHASER2.8.2phasing
BUSTER2.11.7refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DWG

4dwg


Resolution: 1.28→66.179 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.954 / SU R Cruickshank DPI: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.056 / SU Rfree Blow DPI: 0.058 / SU Rfree Cruickshank DPI: 0.055
RfactorNum. reflection% reflectionSelection details
Rfree0.2319 4732 4.9 %RANDOM
Rwork0.209 ---
obs0.21 96670 92.2 %-
Displacement parametersBiso max: 101.1 Å2 / Biso mean: 28.86 Å2 / Biso min: 14.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.4866 Å20 Å20 Å2
2---0.4866 Å20 Å2
3---0.9732 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: final / Resolution: 1.28→66.179 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2863 0 37 264 3164
Biso mean--40.81 37.81 -
Num. residues----359
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1030SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes505HARMONIC5
X-RAY DIFFRACTIONt_it2997HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion380SEMIHARMONIC5
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_contact3876SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2997HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4070HARMONIC20.93
X-RAY DIFFRACTIONt_omega_torsion3.09
X-RAY DIFFRACTIONt_other_torsion15.39
LS refinement shellResolution: 1.28→1.29 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2274 105 5.43 %
Rwork0.2111 1829 -
all0.212 1934 -
obs--99.01 %
Refinement TLS params.Method: refined / Origin x: -9.3662 Å / Origin y: -17.3385 Å / Origin z: -20.0858 Å
111213212223313233
T-0.0544 Å20.026 Å2-0.0048 Å2--0.0057 Å2-0.0162 Å2---0.0274 Å2
L0.7646 °2-0.0795 °2-0.0209 °2-0.2966 °20.0109 °2--0.3517 °2
S-0.0416 Å °-0.1588 Å °0.1318 Å °0.0563 Å °0.0185 Å °-0.0383 Å °-0.0246 Å °0.0472 Å °0.0231 Å °
Refinement TLS groupSelection details: { A|* }

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