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- PDB-6r0a: T. cruzi FPPS in complex with 3-((4-(benzo[d]thiazol-2-yl)piperaz... -

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Basic information

Entry
Database: PDB / ID: 6r0a
TitleT. cruzi FPPS in complex with 3-((4-(benzo[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
ACETATE ION / Chem-JMT / Farnesyl diphosphate synthase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.32 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 / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
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

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Assembly

Deposited unit
A: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3747
Polymers41,3601
Non-polymers1,0156
Water6,539363
1
A: Farnesyl diphosphate synthase
hetero molecules

A: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,74914
Polymers82,7192
Non-polymers2,03012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area7070 Å2
ΔGint-203 kcal/mol
Surface area28890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.191, 58.191, 395.892
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 369 molecules

#2: Chemical ChemComp-JMT / 3-[[4-(1,3-benzothiazol-2-yl)piperazin-1-yl]methyl]-1~{H}-indol-5-ol


Mass: 364.464 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H20N4OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-ZN / ZINC ION


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


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


Mass: 18.015 Da / Num. of mol.: 363 / 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: 0.04 °
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: 1.318→65.982 Å / Num. obs: 95142 / % possible obs: 99.3 % / Redundancy: 18.7 % / Biso Wilson estimate: 22.15 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.018 / Rrim(I) all: 0.077 / Rsym value: 0.074 / Net I/σ(I): 16.7
Reflection shellResolution: 1.318→1.34 Å / Redundancy: 19 % / Rmerge(I) obs: 4.58 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4654 / CC1/2: 0.337 / Rpim(I) all: 1.056 / Rrim(I) all: 4.703 / Rsym value: 4.58 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_TRA
Highest resolutionLowest resolution
Translation3 Å65.98 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: 1.32→65.98 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.957 / SU R Cruickshank DPI: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.057 / SU Rfree Blow DPI: 0.056 / SU Rfree Cruickshank DPI: 0.053
RfactorNum. reflection% reflectionSelection details
Rfree0.2151 4637 4.87 %RANDOM
Rwork0.1982 ---
obs0.199 95139 99.3 %-
Displacement parametersBiso max: 102.71 Å2 / Biso mean: 28.56 Å2 / Biso min: 13.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.2163 Å20 Å20 Å2
2---0.2163 Å20 Å2
3---0.4326 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: final / Resolution: 1.32→65.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2852 0 63 363 3278
Biso mean--36.81 40.82 -
Num. residues----358
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1039SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes514HARMONIC5
X-RAY DIFFRACTIONt_it3041HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion382SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies6HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4137SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3041HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4136HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion3.1
X-RAY DIFFRACTIONt_other_torsion15.91
LS refinement shellResolution: 1.32→1.33 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2327 102 5.36 %
Rwork0.2095 1801 -
all0.2107 1903 -
obs--99.43 %
Refinement TLS params.Method: refined / Origin x: -8.9491 Å / Origin y: -17.4975 Å / Origin z: -20.0527 Å
111213212223313233
T-0.0409 Å20.027 Å2-0.0021 Å2--0.0034 Å2-0.0111 Å2---0.0394 Å2
L0.6179 °2-0.0409 °2-0.0824 °2-0.2543 °2-0.0364 °2--0.3966 °2
S-0.0186 Å °-0.1131 Å °0.0965 Å °0.0432 Å °0.0079 Å °-0.0218 Å °-0.0429 Å °0.0355 Å °0.0106 Å °
Refinement TLS groupSelection details: { A|* }

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