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- PDB-5qtf: T. brucei FPPS in complex with CID 144539 -

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Basic information

Entry
Database: PDB / ID: 5qtf
TitleT. brucei FPPS in complex with CID 144539
ComponentsFarnesyl pyrophosphate synthase
KeywordsTransferase/Transferase inhibitor / farnesyl diphosphate synthase / Trypanosoma brucei / PanDDA / protein-ligand complex / Transferase-Transferase inhibitor complex
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
1-(3-chloro-4-fluorophenyl)methanamine / PHOSPHATE ION / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.783 Å
AuthorsMuenzker, L. / Petrick, J.K. / Schleberger, C. / Cornaciu, I. / Marquez, J.A. / Jahnke, W.
CitationJournal: To Be Published
Title: T. brucei FPPS in complex with CID 144539
Authors: Muenzker, L.
History
DepositionAug 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 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 pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6346
Polymers42,1691
Non-polymers4655
Water1,76598
1
A: Farnesyl pyrophosphate synthase
hetero molecules

A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,26812
Polymers84,3382
Non-polymers92910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area7430 Å2
ΔGint-95 kcal/mol
Surface area28110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.623, 60.623, 341.323
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-534-

HOH

21A-565-

HOH

31A-586-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Farnesyl pyrophosphate synthase


Mass: 42169.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q86C09

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Non-polymers , 5 types, 103 molecules

#2: Chemical ChemComp-PK7 / 1-(3-chloro-4-fluorophenyl)methanamine


Mass: 159.589 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7ClFN
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.15 Å3/Da / Density % sol: 42.71 % / Mosaicity: 0.06 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.12 M CsCl 12 % w/v PEG 3350, 12 % v/v DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.783→56.887 Å / Num. obs: 24054 / % possible obs: 65 % / Redundancy: 36.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.02 / Rrim(I) all: 0.12 / Rsym value: 0.125 / Net I/σ(I): 20.3 / Num. measured all: 811733
Reflection shellResolution: 1.783→2.01 Å / Redundancy: 37.3 % / Rmerge(I) obs: 2.569 / Mean I/σ(I) obs: 1.7 / Num. measured all: 121699 / Num. unique obs: 3167 / CC1/2: 0.985 / Rpim(I) all: 0.325 / Rrim(I) all: 2.029 / Rsym value: 2.569 / Net I/σ(I) obs: 2.3 / % possible all: 11.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.14_3260refinement
Aimless0.7.4data scaling
XDS20180808data reduction
PHASER2.8.2phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 4ryp

4ryp


Resolution: 1.783→56.887 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 38.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2931 1192 4.96 %
Rwork0.2503 22856 -
obs0.2525 24048 65.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.58 Å2 / Biso mean: 53.2114 Å2 / Biso min: 14.84 Å2
Refinement stepCycle: final / Resolution: 1.783→56.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2629 0 27 98 2754
Biso mean--83.7 52.08 -
Num. residues----330
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7829-1.85430.513170.37081481554
1.8543-1.93870.3075210.37538240310
1.9387-2.04090.4047410.3485981102225
2.0409-2.16880.3204980.30571989208751
2.1688-2.33630.34021790.31633294347386
2.3363-2.57140.33582030.288438594062100
2.5714-2.94340.29222060.282639124118100
2.9434-3.70830.29362100.246839894199100
3.7083-56.91610.26812270.210543024529100

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