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- PDB-6r37: T. brucei FPPS in complex with 2-(5-chlorobenzo[b]thiophen-3-yl)a... -

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Basic information

Entry
Database: PDB / ID: 6r37
TitleT. brucei FPPS in complex with 2-(5-chlorobenzo[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
(5-chloro-1-benzothiophen-3-yl)acetic acid / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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.
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 / citation_author / 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 / pdbx_initial_refinement_model

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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)42,4743
Polymers42,1691
Non-polymers3052
Water00
1
A: Farnesyl pyrophosphate synthase
hetero molecules

A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9486
Polymers84,3382
Non-polymers6104
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area6040 Å2
ΔGint-21 kcal/mol
Surface area27650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.769, 60.769, 341.204
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 BL21(DE3) (bacteria) / References: UniProt: Q86C09
#2: Chemical ChemComp-3N2 / (5-chloro-1-benzothiophen-3-yl)acetic acid


Mass: 226.679 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H7ClO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM

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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: 43.17 % / Description: thin needles
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 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99996 Å / Relative weight: 1
ReflectionResolution: 2.1→52.628 Å / Num. obs: 21086 / % possible obs: 91.3 % / Redundancy: 18.2 % / Biso Wilson estimate: 56.15 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.02 / Rrim(I) all: 0.083 / Rsym value: 0.08 / Net I/σ(I): 19.4
Reflection shellResolution: 2.1→2.136 Å / Redundancy: 17.4 % / Rmerge(I) obs: 4.686 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1075 / CC1/2: 0.466 / Rpim(I) all: 1.135 / Rrim(I) all: 4.827 / Rsym value: 4.686 / % possible all: 98.9

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Processing

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

4ryp


Resolution: 2.1→52.628 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.257 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.268 / SU Rfree Blow DPI: 0.198 / SU Rfree Cruickshank DPI: 0.195
RfactorNum. reflection% reflectionSelection details
Rfree0.2564 1055 5 %RANDOM
Rwork0.2382 ---
obs0.239 21086 91.3 %-
Displacement parametersBiso max: 219.29 Å2 / Biso mean: 92.83 Å2 / Biso min: 44.87 Å2
Baniso -1Baniso -2Baniso -3
1--7.4648 Å20 Å20 Å2
2---7.4648 Å20 Å2
3---14.9296 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: final / Resolution: 2.1→52.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2628 0 18 0 2646
Biso mean--103.92 --
Num. residues----329
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d943SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes453HARMONIC5
X-RAY DIFFRACTIONt_it2696HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion339SEMIHARMONIC5
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_contact3106SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2696HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3640HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion2.45
X-RAY DIFFRACTIONt_other_torsion18.14
LS refinement shellResolution: 2.1→2.11 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.219 18 4.27 %
Rwork0.2165 404 -
all0.2167 422 -
obs--96.51 %
Refinement TLS params.Method: refined / Origin x: 3.2875 Å / Origin y: 11.8605 Å / Origin z: -11.2889 Å
111213212223313233
T0.0992 Å20.0318 Å2-0.1385 Å2--0.2056 Å20.0054 Å2---0.3118 Å2
L0.5686 °20.0331 °2-1.0136 °2-3.0123 °22.7444 °2--6.9523 °2
S-0.2547 Å °0.0855 Å °0.0117 Å °-0.8274 Å °0.0422 Å °0.3377 Å °-1.1235 Å °-0.2311 Å °0.2125 Å °
Refinement TLS groupSelection details: { A|* }

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