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

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Basic information

Entry
Database: PDB / ID: 5qpf
TitlePanDDA analysis group deposition -- Crystal Structure of T. cruzi FPPS in complex with FMOPL000478a
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 / 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
ACETATE ION / 2-(4-methylpiperazin-1-yl)-1,3-benzothiazole / Farnesyl diphosphate synthase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.5 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)42,3049
Polymers41,3601
Non-polymers9458
Water5,945330
1
A: Farnesyl diphosphate synthase
hetero molecules

A: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,60918
Polymers82,7192
Non-polymers1,88916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area8060 Å2
ΔGint-292 kcal/mol
Surface area28280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.900, 57.900, 395.156
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 338 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-AWM / 2-(4-methylpiperazin-1-yl)-1,3-benzothiazole


Mass: 233.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H15N3S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 46.79 % / 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: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→98.82 Å / Num. obs: 65050 / % possible obs: 100 % / Redundancy: 16.6 % / Biso Wilson estimate: 15.52 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.03 / Rrim(I) all: 0.126 / Net I/σ(I): 12.9 / Num. measured all: 1078620 / Scaling rejects: 1754
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
1.5-1.5411.82.135492146730.5440.6482.2281.4
6.71-98.8214.20.046137909700.9980.0130.04837

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1YHK

1yhk


Resolution: 1.5→49.744 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2483 3343 5.2 %
Rwork0.2132 60915 -
obs0.215 64258 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.1 Å2 / Biso mean: 22.1799 Å2 / Biso min: 5.36 Å2
Refinement stepCycle: final / Resolution: 1.5→49.744 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2871 0 53 331 3255
Biso mean--36.06 30.97 -
Num. residues----360
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4997-1.52110.39341180.34132463258197
1.5211-1.54390.30221430.34162421256499
1.5439-1.5680.43011440.33862496264099
1.568-1.59370.35441500.31312428257899
1.5937-1.62120.32921420.30532465260799
1.6212-1.65060.29771560.28072482263899
1.6506-1.68240.37041280.27192460258899
1.6824-1.71670.31311540.2692467262199
1.7167-1.75410.28851370.26042513265099
1.7541-1.79490.2871260.24962482260899
1.7949-1.83980.34521190.24652516263599
1.8398-1.88950.28021330.24022508264199
1.8895-1.94510.25961180.23572539265799
1.9451-2.00790.2541370.23122525266299
2.0079-2.07970.27041280.22292509263799
2.0797-2.16290.26561330.21262527266099
2.1629-2.26140.21831280.20942540266899
2.2614-2.38060.24821690.20082535270499
2.3806-2.52970.26971580.20092547270599
2.5297-2.7250.2431470.20062572271999
2.725-2.99920.22991270.19652617274499
2.9992-3.43320.2081460.18726492795100
3.4332-4.3250.19271400.168327092849100
4.325-49.77150.20261620.182929453107100

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