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- PDB-5qqc: Crystal Structure of T. cruzi FPPS after initial refinement with ... -

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Basic information

Entry
Database: PDB / ID: 5qqc
TitleCrystal Structure of T. cruzi FPPS after initial refinement with no ligand modelled (structure $n)
ComponentsFarnesyl diphosphate synthase
KeywordsTRANSFERASE / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer
Function / homology
Function and homology information


prenyltransferase activity / isoprenoid biosynthetic process / membrane / metal ion binding
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
ACETATE ION / Farnesyl diphosphate synthase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.62 Å
AuthorsPetrick, J.K. / Nelson, E.R. / Muenzker, L. / Krojer, T. / Douangamath, A. / Brandao-Neto, J. / von Delft, F. / Dekker, C. / Jahnke, W.
CitationJournal: To Be Published
Title: PanDDA analysis group deposition of ground-state model - FPPS screened against the DSI Fragment Library
Authors: Petrick, J.K. / Muenzker, L. / von Delft, F. / Jahnke, W.
History
DepositionMar 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6596
Polymers41,3601
Non-polymers3005
Water5,242291
1
A: Farnesyl diphosphate synthase
hetero molecules

A: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,31912
Polymers82,7192
Non-polymers60010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area7630 Å2
ΔGint-130 kcal/mol
Surface area28380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.681, 57.681, 396.512
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
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WS26
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.3 Å3/Da / Density % sol: 46.57 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 80 mM MES, 4 mM ZnSO4, 12.36% w/v PEG MME 550, 11.57% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.62→132.19 Å / Num. obs: 51799 / % possible obs: 100 % / Redundancy: 17.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.024 / Rrim(I) all: 0.103 / Net I/σ(I): 15 / Num. measured all: 915855 / Scaling rejects: 434
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.62-1.6614.92.7345561337330.5230.732.8311.2
7.24-132.1914.20.037109567740.9980.010.03951

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0189refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1YHK

1yhk


Resolution: 1.62→66.09 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.377 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2274 2650 5.2 %RANDOM
Rwork0.1916 ---
obs0.1934 48589 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.74 Å2 / Biso mean: 30.73 Å2 / Biso min: 14.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.62→66.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2871 0 16 292 3179
Biso mean--45.3 40.93 -
Num. residues----360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192953
X-RAY DIFFRACTIONr_bond_other_d0.0020.022735
X-RAY DIFFRACTIONr_angle_refined_deg2.0151.9554003
X-RAY DIFFRACTIONr_angle_other_deg1.10336334
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.365361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.01724.338136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23515511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1881515
X-RAY DIFFRACTIONr_chiral_restr0.1250.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023265
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02614
X-RAY DIFFRACTIONr_mcbond_it2.7292.7721442
X-RAY DIFFRACTIONr_mcbond_other2.7282.7671440
X-RAY DIFFRACTIONr_mcangle_it3.6734.1461800
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 202 -
Rwork0.353 3436 -
all-3638 -
obs--97.72 %

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