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- PDB-6r08: T. cruzi FPPS in complex with 3-(carboxymethyl)-5,7-dichloro-1H-i... -

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Basic information

Entry
Database: PDB / ID: 6r08
TitleT. cruzi FPPS in complex with 3-(carboxymethyl)-5,7-dichloro-1H-indole-2-carboxylic acid
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
Chem-GO1 / Farnesyl diphosphate synthase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.44 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 / Category: citation / citation_author / 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 / _citation_author.name / _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)41,8755
Polymers41,3601
Non-polymers5154
Water6,035335
1
A: Farnesyl diphosphate synthase
hetero molecules

A: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,74910
Polymers82,7192
Non-polymers1,0308
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area6810 Å2
ΔGint-194 kcal/mol
Surface area28600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.895, 57.895, 398.225
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 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
#2: Chemical ChemComp-GO1 / 3-(carboxymethyl)-5,7-dichloro-1H-indole-2-carboxylic acid


Mass: 288.084 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H7Cl2NO4 / 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.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.33 Å3/Da / Density % sol: 47.19 % / Mosaicity: 0.06 °
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: 0.99985 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99985 Å / Relative weight: 1
ReflectionResolution: 1.435→49.746 Å / Num. obs: 74408 / % possible obs: 100 % / Redundancy: 18.7 % / Biso Wilson estimate: 28.12 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.013 / Rrim(I) all: 0.055 / Rsym value: 0.053 / Net I/σ(I): 23.1
Reflection shellResolution: 1.435→1.459 Å / Redundancy: 19.5 % / Rmerge(I) obs: 4.737 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 3629 / CC1/2: 0.362 / Rpim(I) all: 1.094 / Rrim(I) all: 4.863 / Rsym value: 4.737 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_TRA
Highest resolutionLowest resolution
Translation3 Å49.75 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: 1.44→48.62 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.96 / SU R Cruickshank DPI: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.069 / SU Rfree Blow DPI: 0.069 / SU Rfree Cruickshank DPI: 0.065
RfactorNum. reflection% reflectionSelection details
Rfree0.213 3628 4.88 %RANDOM
Rwork0.1906 ---
obs0.192 74407 100 %-
Displacement parametersBiso max: 110.25 Å2 / Biso mean: 35.92 Å2 / Biso min: 19.33 Å2
Baniso -1Baniso -2Baniso -3
1--1.5506 Å20 Å20 Å2
2---1.5506 Å20 Å2
3---3.1012 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: final / Resolution: 1.44→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2868 0 25 335 3228
Biso mean--50.96 47.68 -
Num. residues----360
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1065SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes526HARMONIC5
X-RAY DIFFRACTIONt_it3059HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion388SEMIHARMONIC5
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_contact4117SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3059HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4164HARMONIC20.9
X-RAY DIFFRACTIONt_omega_torsion2.95
X-RAY DIFFRACTIONt_other_torsion15.07
LS refinement shellResolution: 1.44→1.45 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2294 79 5.31 %
Rwork0.2107 1410 -
all0.2117 1489 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -8.8008 Å / Origin y: -17.3607 Å / Origin z: -20.4514 Å
111213212223313233
T-0.0563 Å20.0248 Å2-0.003 Å2--0.0102 Å2-0.0228 Å2---0.0438 Å2
L1.0009 °2-0.0923 °2-0.0024 °2-0.3596 °20.004 °2--0.3467 °2
S-0.0416 Å °-0.1847 Å °0.1637 Å °0.0609 Å °0.0121 Å °-0.0406 Å °-0.0166 Å °0.0342 Å °0.0295 Å °
Refinement TLS groupSelection details: { A|* }

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