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

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Basic information

Entry
Database: PDB / ID: 5qpo
TitlePanDDA analysis group deposition -- Crystal Structure of T. cruzi FPPS in complex with FMOPL000574a
ComponentsFarnesyl diphosphate synthase
KeywordsTRANSFERASE / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer
Function / homology
Function and homology information


farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / membrane / 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
ACETATE ION / 1-[(4-fluorophenyl)methyl]benzimidazole / 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)41,8375
Polymers41,3601
Non-polymers4774
Water5,891327
1
A: Farnesyl diphosphate synthase
hetero molecules

A: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,67410
Polymers82,7192
Non-polymers9558
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area7400 Å2
ΔGint-108 kcal/mol
Surface area28470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.894, 57.894, 395.786
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-GQP / 1-[(4-fluorophenyl)methyl]benzimidazole


Mass: 226.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H11FN2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.31 Å3/Da / Density % sol: 46.86 % / 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 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.6→198.04 Å / Num. obs: 54030 / % possible obs: 100 % / Redundancy: 17.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.212 / Rpim(I) all: 0.051 / Rrim(I) all: 0.218 / Net I/σ(I): 7.6 / Num. measured all: 941087 / Scaling rejects: 2010
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
1.6-1.6414.52.6425614138800.5380.7152.7391
7.16-198.0413.90.0711130381410.0180.07316

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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→65.96 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.759 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2688 2688 5.2 %RANDOM
Rwork0.2265 ---
obs0.2287 49443 96.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.02 Å2 / Biso mean: 18.808 Å2 / Biso min: 5.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å20 Å2
2--0.03 Å20 Å2
3----0.09 Å2
Refinement stepCycle: final / Resolution: 1.6→65.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2871 0 31 328 3230
Biso mean--36.5 27.95 -
Num. residues----360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.023320
X-RAY DIFFRACTIONr_bond_other_d0.0020.022899
X-RAY DIFFRACTIONr_angle_refined_deg2.011.9684296
X-RAY DIFFRACTIONr_angle_other_deg1.13436732
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3575392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.50524.444144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.9415548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8981515
X-RAY DIFFRACTIONr_chiral_restr0.1350.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023763
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02676
X-RAY DIFFRACTIONr_mcbond_it1.6931.7011610
X-RAY DIFFRACTIONr_mcbond_other1.6931.7021611
X-RAY DIFFRACTIONr_mcangle_it2.5142.5131932
LS refinement shellResolution: 1.599→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 205 -
Rwork0.349 3383 -
all-3588 -
obs--92.62 %

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