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- PDB-6r39: T. brucei FPPS in complex with 1-(carboxymethyl)-1H-benzo[g]indol... -

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Basic information

Entry
Database: PDB / ID: 6r39
TitleT. brucei FPPS in complex with 1-(carboxymethyl)-1H-benzo[g]indole-2-carboxylic 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-BFH / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 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 farnesyl pyrophosphate synthase of Trypanosoma cruzi by fragment-based lead discovery
Authors: Petrick, J.K. / Jahnke, W.
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 1.2Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.3Feb 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 pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4382
Polymers42,1691
Non-polymers2691
Water362
1
A: Farnesyl pyrophosphate synthase
hetero molecules

A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,8774
Polymers84,3382
Non-polymers5392
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area4480 Å2
ΔGint-26 kcal/mol
Surface area27890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.336, 61.336, 340.077
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-BFH / 1-(carboxymethyl)-1H-benzo[g]indole-2-carboxylic acid


Mass: 269.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H11NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.19 Å3/Da / Density % sol: 43.83 %
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: 1.00001 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.552→53.119 Å / Num. obs: 13351 / % possible obs: 100 % / Redundancy: 18.3 % / Biso Wilson estimate: 74.43 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.036 / Rrim(I) all: 0.152 / Rsym value: 0.148 / Net I/σ(I): 14.4
Reflection shellResolution: 2.552→2.596 Å / Redundancy: 19.6 % / Rmerge(I) obs: 7.207 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 629 / CC1/2: 0.539 / Rpim(I) all: 1.658 / Rrim(I) all: 7.399 / Rsym value: 7.207 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_TRA
Highest resolutionLowest resolution
Translation3 Å53.12 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: 2.6→14.96 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.688 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.892 / SU Rfree Blow DPI: 0.31 / SU Rfree Cruickshank DPI: 0.304
RfactorNum. reflection% reflectionSelection details
Rfree0.2571 630 5.01 %RANDOM
Rwork0.2343 ---
obs0.235 12572 100 %-
Displacement parametersBiso max: 228.05 Å2 / Biso mean: 127.85 Å2 / Biso min: 70.06 Å2
Baniso -1Baniso -2Baniso -3
1--6.8291 Å20 Å20 Å2
2---6.8291 Å20 Å2
3---13.6581 Å2
Refine analyzeLuzzati coordinate error obs: 0.52 Å
Refinement stepCycle: final / Resolution: 2.6→14.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2612 0 20 2 2634
Biso mean--133.38 70.57 -
Num. residues----327
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d938SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes449HARMONIC5
X-RAY DIFFRACTIONt_it2684HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion338SEMIHARMONIC5
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_contact3153SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2684HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3627HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion2.44
X-RAY DIFFRACTIONt_other_torsion19.42
LS refinement shellResolution: 2.6→2.63 Å / Rfactor Rfree error: 0 / Total num. of bins used: 31
RfactorNum. reflection% reflection
Rfree0.1966 23 5.67 %
Rwork0.2179 383 -
all0.2165 406 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 3.4802 Å / Origin y: 12.5257 Å / Origin z: -11.4152 Å
111213212223313233
T0.5864 Å20.0915 Å20.062 Å2--0.0734 Å20.1246 Å2---0.4297 Å2
L0.2359 °20.6539 °20.6879 °2-2.886 °21.3622 °2--8.2528 °2
S-0.4893 Å °0.0347 Å °-0.0262 Å °-0.5248 Å °0.5573 Å °0.1068 Å °-1.1941 Å °-0.1088 Å °-0.068 Å °
Refinement TLS groupSelection details: { A|* }

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