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- PDB-6sii: T. brucei FPPS in complex with 1-((1H-indol-3-yl)methyl)-N-(3-chl... -

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Basic information

Entry
Database: PDB / ID: 6sii
TitleT. brucei FPPS in complex with 1-((1H-indol-3-yl)methyl)-N-(3-chlorobenzyl)piperidin-4-amine
ComponentsFarnesyl pyrophosphate synthase
KeywordsTRANSFERASE / sterol biosynthesis / homodimer / farnesyl pyrophosphate synthase / Trypanosoma brucei
Function / homology
Function and homology information


prenyltransferase activity / isoprenoid biosynthetic process / metal ion binding
Similarity search - Function
Farnesyl pyrophosphate synthase-like / Polyprenyl synthases signature 2. / Polyprenyl synthases signature 1. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
Chem-LEZ / 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, 2items
OrganizationGrant numberCountry
Other government675899 Switzerland
Marie Sklodowska-Curie Actions, FragNET ITN
CitationJournal: To Be Published
Title: T. brucei FPPS
Authors: Muenzker, L. / Jahnke, W.
History
DepositionAug 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)42,6153
Polymers42,1691
Non-polymers4462
Water00
1
A: Farnesyl pyrophosphate synthase
hetero molecules

A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2306
Polymers84,3382
Non-polymers8924
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area5730 Å2
ΔGint-34 kcal/mol
Surface area28250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.631, 61.631, 342.247
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-LEZ / ~{N}-[(3-chlorophenyl)methyl]-1-(1~{H}-indol-3-ylmethyl)piperidin-4-amine


Mass: 353.888 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24ClN3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
Has ligand of interestY

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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: 2.22 Å3/Da / Density % sol: 44.71 % / Description: needles
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.12 M CsCl 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: 1.00002 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.326→57.041 Å / Num. obs: 17624 / % possible obs: 99.4 % / Redundancy: 18.5 % / Biso Wilson estimate: 79.33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.027 / Rrim(I) all: 0.116 / Rsym value: 0.113 / Net I/σ(I): 15.1 / Num. measured all: 326497
Reflection shellResolution: 2.326→2.366 Å / Redundancy: 19.6 % / Rmerge(I) obs: 12.631 / Mean I/σ(I) obs: 0.3 / Num. measured all: 48808 / Num. unique obs: 2512 / CC1/2: 0.59 / Rpim(I) all: 1.983 / Rrim(I) all: 8.823 / Rsym value: 12.631 / Net I/σ(I) obs: 0.4 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_TRA
Highest resolutionLowest resolution
Translation3 Å57.04 Å

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Processing

Software
NameVersionClassification
BUSTERrefinement
XDS20180126data reduction
Aimless0.7.4data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 4ryp

4ryp


Resolution: 2.33→57.04 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.394 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.429 / SU Rfree Blow DPI: 0.266 / SU Rfree Cruickshank DPI: 0.261
RfactorNum. reflection% reflectionSelection details
Rfree0.276 832 5.01 %RANDOM
Rwork0.25 ---
obs0.252 16603 93.6 %-
Displacement parametersBiso max: 228.35 Å2 / Biso mean: 121.49 Å2 / Biso min: 64.15 Å2
Baniso -1Baniso -2Baniso -3
1--4.1842 Å20 Å20 Å2
2---4.1842 Å20 Å2
3---8.3684 Å2
Refine analyzeLuzzati coordinate error obs: 0.49 Å
Refinement stepCycle: final / Resolution: 2.33→57.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2619 0 31 0 2650
Biso mean--119.51 --
Num. residues----328
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d949SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes471HARMONIC5
X-RAY DIFFRACTIONt_it2702HARMONIC20
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_contact3115SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2702HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3648HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion2.38
X-RAY DIFFRACTIONt_other_torsion18.44
LS refinement shellResolution: 2.33→2.38 Å / Rfactor Rfree error: 0 / Total num. of bins used: 41
RfactorNum. reflection% reflection
Rfree0.6311 17 4.2 %
Rwork0.3485 388 -
all0.3606 405 -
obs--36.88 %
Refinement TLS params.Method: refined / Origin x: 3.4606 Å / Origin y: 11.916 Å / Origin z: -11.451 Å
111213212223313233
T0.3582 Å2-0.0271 Å2-0.0133 Å2--0.1289 Å20.0896 Å2---0.3311 Å2
L1.0762 °20.245 °2-1.2262 °2-2.5632 °21.3147 °2--12.6176 °2
S-0.367 Å °0.1769 Å °0.0524 Å °-0.3433 Å °0.5399 Å °0.1587 Å °-1.2298 Å °-0.0469 Å °-0.1729 Å °
Refinement TLS groupSelection details: { A|* }

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