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- PDB-5qpv: PanDDA analysis group deposition -- Crystal Structure of T. cruzi... -

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Basic information

Entry
Database: PDB / ID: 5qpv
TitlePanDDA analysis group deposition -- Crystal Structure of T. cruzi FPPS in complex with FMOPL000416a
ComponentsFarnesyl diphosphate synthase
KeywordsTRANSFERASE / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer
Function / homology
Function and homology information


transferase activity, transferring alkyl or aryl (other than methyl) groups / 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
Chem-LWA / Farnesyl diphosphate synthase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.6 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 - FPPS screened against the DSI Fragment Library
Authors: Petrick, J.K. / Muenzker, L. / von Delft, F. / Jahnke, W.
History
DepositionMar 12, 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)42,0866
Polymers41,3601
Non-polymers7265
Water5,621312
1
A: Farnesyl diphosphate synthase
hetero molecules

A: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,17112
Polymers82,7192
Non-polymers1,45210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area6860 Å2
ΔGint-156 kcal/mol
Surface area28600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.831, 57.831, 397.468
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 / Sulfate


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


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-LWA / (2~{S})-~{N}-(4-aminocarbonylphenyl)oxolane-2-carboxamide


Mass: 234.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H14N2O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O
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: 2.32 Å3/Da / Density % sol: 46.97 % / 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: 1.6→132.49 Å / Num. obs: 54109 / % possible obs: 100 % / Redundancy: 17.6 % / CC1/2: 0.979 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.028 / Rrim(I) all: 0.117 / Net I/σ(I): 14.1 / Num. measured all: 954926 / Scaling rejects: 405
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
1.6-1.6414.62.3815697938900.5830.6392.4671.4
7.16-132.4914.30.039115128070.9590.0120.04144.8

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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: 1.6→66.24 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.568 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2367 2769 5.2 %RANDOM
Rwork0.1955 ---
obs0.1976 50836 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 218.31 Å2 / Biso mean: 28.93 Å2 / Biso min: 6.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.08 Å20 Å2
2--0.15 Å20 Å2
3----0.49 Å2
Refinement stepCycle: final / Resolution: 1.6→66.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2871 0 45 312 3228
Biso mean--33.61 39.32 -
Num. residues----360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.024551
X-RAY DIFFRACTIONr_bond_other_d0.0020.023585
X-RAY DIFFRACTIONr_angle_refined_deg21.9795300
X-RAY DIFFRACTIONr_angle_other_deg1.11538328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.585482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02323.389180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11715686
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5691527
X-RAY DIFFRACTIONr_chiral_restr0.1310.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024626
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02873
X-RAY DIFFRACTIONr_mcbond_it2.6942.6532155
X-RAY DIFFRACTIONr_mcbond_other2.3942.4872085
X-RAY DIFFRACTIONr_mcangle_it3.6563.732356
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 217 -
Rwork0.349 3618 -
all-3835 -
obs--98.64 %

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