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- PDB-6r38: T. brucei FPPS in complex with 2-(2,5-dichlorobenzo[b]thiophen-3-... -

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Basic information

Entry
Database: PDB / ID: 6r38
TitleT. brucei FPPS in complex with 2-(2,5-dichlorobenzo[b]thiophen-3-yl)acetic acid
ComponentsFarnesyl pyrophosphate synthase
KeywordsTRANSFERASE / sterol biosynthesis / farnesyl diphosphate synthase / Trypanosoma brucei / homodimer
Function / homology
Function and homology information


farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / 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-JQE / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.33 Å
AuthorsMuenzker, L. / Petrick, J.K. / Schleberger, C. / Jahnke, W.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Marie Sklodowska-Curie Actions, FragNET ITN675899 Switzerland
CitationJournal: Thesis / Year: 2019
Title: Targeting Trypanosoma brucei FPPS by Fragment-based drug discovery
Authors: Muenzker, L. / Wolfgang, J.
History
DepositionMar 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / refine
Item: _refine.pdbx_diffrn_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5083
Polymers42,1691
Non-polymers3392
Water181
1
A: Farnesyl pyrophosphate synthase
hetero molecules

A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,0176
Polymers84,3382
Non-polymers6794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area5920 Å2
ΔGint-23 kcal/mol
Surface area27610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.839, 60.839, 339.990
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 pyrophosphate synthase


Mass: 42169.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GP is an expression tag / Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q86C09
#2: Chemical ChemComp-JQE / 2-[2,5-bis(chloranyl)-1-benzothiophen-3-yl]ethanoic acid


Mass: 261.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H6Cl2O2S
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.16 Å3/Da / Density % sol: 43.1 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.12 M Cesium chloride, 12 %w/v PEG 3350, 12 % v/v DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99996 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99996 Å / Relative weight: 1
ReflectionResolution: 2.33→56.665 Å / Num. obs: 17098 / % possible obs: 100 % / Redundancy: 18.6 % / Biso Wilson estimate: 50.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.328 / Rpim(I) all: 0.077 / Rrim(I) all: 0.337 / Rsym value: 0.328 / Net I/σ(I): 9.5
Reflection shellResolution: 2.33→2.37 Å / Redundancy: 19.8 % / Rmerge(I) obs: 11.166 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 812 / CC1/2: 0.458 / Rpim(I) all: 2.541 / Rrim(I) all: 11.456 / Rsym value: 11.166 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_TRA
Highest resolutionLowest resolution
Translation3 Å56.66 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: 4ryp

4ryp


Resolution: 2.33→56.66 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.923 / SU R Cruickshank DPI: 0.334 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.361 / SU Rfree Blow DPI: 0.232 / SU Rfree Cruickshank DPI: 0.228
RfactorNum. reflection% reflectionSelection details
Rfree0.2491 860 5.03 %RANDOM
Rwork0.2239 ---
obs0.225 17097 100 %-
Displacement parametersBiso max: 185.75 Å2 / Biso mean: 84.44 Å2 / Biso min: 38.54 Å2
Baniso -1Baniso -2Baniso -3
1--7.7836 Å20 Å20 Å2
2---7.7836 Å20 Å2
3---15.5672 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: final / Resolution: 2.33→56.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2643 0 19 1 2663
Biso mean--93.93 62.31 -
Num. residues----331
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d948SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes455HARMONIC5
X-RAY DIFFRACTIONt_it2712HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion343SEMIHARMONIC5
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_contact3198SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2712HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3663HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion2.54
X-RAY DIFFRACTIONt_other_torsion17.75
LS refinement shellResolution: 2.33→2.35 Å / Rfactor Rfree error: 0 / Total num. of bins used: 43
RfactorNum. reflection% reflection
Rfree0.2371 24 6.03 %
Rwork0.2192 374 -
all0.2204 398 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 3.3957 Å / Origin y: 11.8045 Å / Origin z: -11.3262 Å
111213212223313233
T0.1138 Å20.0451 Å2-0.1033 Å2--0.1448 Å2-0.0019 Å2---0.3219 Å2
L0.8937 °20.0326 °2-1.0672 °2-2.2302 °22.2352 °2--6.5379 °2
S-0.1838 Å °0.1573 Å °0.0257 Å °-0.6848 Å °0.0018 Å °0.2571 Å °-1.0346 Å °-0.385 Å °0.182 Å °
Refinement TLS groupSelection details: { A|* }

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