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- PDB-6r06: T. CRUZI FPPS IN COMPLEX WITH (3S,4S)-4-(3,4-dimethylphenoxy)-1-(... -

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Basic information

Entry
Database: PDB / ID: 6r06
TitleT. CRUZI FPPS IN COMPLEX WITH (3S,4S)-4-(3,4-dimethylphenoxy)-1-(prop-2-yn-1-yl)piperidin-3-ol
ComponentsFarnesyl diphosphate synthase
KeywordsTRANSFERASE / farnesyl diphosphate synthase / sterol biosynthesis / farnesyl pyrophosphate / homodimer
Function / homology
Function and homology information


prenyltransferase activity / isoprenoid biosynthetic process / membrane / metal ion binding
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-JMN / Farnesyl diphosphate synthase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.559 Å
AuthorsPetrick, J.K. / Muenzker, L. / Schleberger, C. / Wolfgang, J.
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 / 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 / _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)42,2608
Polymers41,3601
Non-polymers9017
Water4,486249
1
A: Farnesyl diphosphate synthase
hetero molecules

A: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,52016
Polymers82,7192
Non-polymers1,80114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area7740 Å2
ΔGint-269 kcal/mol
Surface area28560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.065, 58.065, 397.506
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, 256 molecules

#2: Chemical ChemComp-JMN / (3~{S},4~{S})-4-(3,4-dimethylphenoxy)-1-prop-2-ynyl-piperidin-3-ol


Mass: 259.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H21NO2 / 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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 47.4 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 80 mM MES: 8.5 mM ZnSO4: 19.42 % PEG MME 550: 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.559→50.286 Å / Num. obs: 58053 / % possible obs: 99 % / Redundancy: 17.8 % / Biso Wilson estimate: 28.19 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.024 / Rrim(I) all: 0.1 / Rsym value: 0.097 / Net I/σ(I): 15.5
Reflection shellResolution: 1.559→1.586 Å / Redundancy: 18.1 % / Rmerge(I) obs: 3.043 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2851 / CC1/2: 0.342 / Rpim(I) all: 0.731 / Rrim(I) all: 3.13 / Rsym value: 3.043 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_TRA
Highest resolutionLowest resolution
Translation3 Å50.29 Å

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Processing

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

4dwg


Resolution: 1.559→50.286 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.945 / SU R Cruickshank DPI: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.087 / SU Rfree Blow DPI: 0.086 / SU Rfree Cruickshank DPI: 0.082
RfactorNum. reflection% reflectionSelection details
Rfree0.2236 2865 4.94 %RANDOM
Rwork0.1954 ---
obs0.197 58053 99 %-
Displacement parametersBiso max: 111.65 Å2 / Biso mean: 36.93 Å2 / Biso min: 15.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.8924 Å20 Å20 Å2
2--0.8924 Å20 Å2
3----1.7849 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: final / Resolution: 1.559→50.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2871 0 54 249 3174
Biso mean--39 43.53 -
Num. residues----360
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1047SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes510HARMONIC5
X-RAY DIFFRACTIONt_it3035HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion387SEMIHARMONIC5
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_contact4027SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3035HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4120HARMONIC20.88
X-RAY DIFFRACTIONt_omega_torsion2.66
X-RAY DIFFRACTIONt_other_torsion15.81
LS refinement shellResolution: 1.56→1.57 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2329 54 4.65 %
Rwork0.2193 1108 -
all0.2199 1162 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -9.908 Å / Origin y: -17.0261 Å / Origin z: -20.4152 Å
111213212223313233
T-0.0727 Å20.0404 Å20.0005 Å2--0.0093 Å2-0.0337 Å2---0.0839 Å2
L1.5086 °2-0.1365 °2-0.0961 °2-0.5489 °2-0.0392 °2--0.5117 °2
S-0.042 Å °-0.3036 Å °0.2236 Å °0.0795 Å °0.0286 Å °-0.0461 Å °-0.0409 Å °0.0229 Å °0.0134 Å °
Refinement TLS groupSelection details: { A|* }

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