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- PDB-6r0b: T. cruzi FPPS in complex with 3-((4-(5-chlorobenzo[d]thiazol-2-yl... -

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Basic information

Entry
Database: PDB / ID: 6r0b
TitleT. cruzi FPPS in complex with 3-((4-(5-chlorobenzo[d]thiazol-2-yl)piperazin-1-yl)methyl)-1H-indol-5-ol
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 / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-JMW / Farnesyl diphosphate synthase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.612 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)42,0165
Polymers41,3601
Non-polymers6564
Water5,008278
1
A: Farnesyl diphosphate synthase
hetero molecules

A: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,03210
Polymers82,7192
Non-polymers1,3138
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area7020 Å2
ΔGint-167 kcal/mol
Surface area28740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.094, 58.094, 396.952
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-JMW / 3-[[4-(5-chloranyl-1,3-benzothiazol-2-yl)piperazin-1-yl]methyl]-1~{H}-indol-5-ol


Mass: 398.909 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19ClN4OS / 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.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 47.38 % / Mosaicity: 0.12 °
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: 1.00003 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.612→50.311 Å / Num. obs: 52572 / % possible obs: 98.9 % / Redundancy: 18 % / Biso Wilson estimate: 31.12 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.023 / Rrim(I) all: 0.095 / Rsym value: 0.092 / Net I/σ(I): 16.9
Reflection shellResolution: 1.612→1.639 Å / Redundancy: 17.5 % / Rmerge(I) obs: 3.595 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2540 / CC1/2: 0.318 / Rpim(I) all: 0.881 / Rrim(I) all: 3.703 / Rsym value: 3.595 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_TRA
Highest resolutionLowest resolution
Translation3 Å50.31 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: 1.612→50.31 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU R Cruickshank DPI: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.094 / SU Rfree Blow DPI: 0.096 / SU Rfree Cruickshank DPI: 0.092
RfactorNum. reflection% reflectionSelection details
Rfree0.2295 2591 4.95 %RANDOM
Rwork0.1906 ---
obs0.193 52297 98.4 %-
Displacement parametersBiso max: 122.97 Å2 / Biso mean: 36.38 Å2 / Biso min: 19.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.1355 Å20 Å20 Å2
2--0.1355 Å20 Å2
3----0.271 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 1.612→50.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2852 0 38 278 3168
Biso mean--56.81 45.03 -
Num. residues----358
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1022SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes500HARMONIC5
X-RAY DIFFRACTIONt_it2981HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion378SEMIHARMONIC5
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_contact3867SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2981HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4048HARMONIC20.9
X-RAY DIFFRACTIONt_omega_torsion2.7
X-RAY DIFFRACTIONt_other_torsion16.07
LS refinement shellResolution: 1.61→1.62 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.1938 48 4.59 %
Rwork0.1988 998 -
all0.1985 1046 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -9.0635 Å / Origin y: -17.3684 Å / Origin z: -20.2264 Å
111213212223313233
T-0.0289 Å20.0227 Å2-0.0044 Å2-0.0106 Å2-0.022 Å2---0.0877 Å2
L0.9784 °2-0.0401 °2-0.1924 °2-0.2808 °2-0.055 °2--0.4502 °2
S-0.0234 Å °-0.1841 Å °0.1303 Å °0.0421 Å °0.0107 Å °-0.0231 Å °-0.056 Å °0.0358 Å °0.0127 Å °
Refinement TLS groupSelection details: { A|* }

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