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- PDB-5qte: T. brucei FPPS in complex with CID 4563894 -

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Basic information

Entry
Database: PDB / ID: 5qte
TitleT. brucei FPPS in complex with CID 4563894
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


farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / 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 / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
Chem-PKD / PHOSPHATE ION / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.072 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 4563894
Authors: Muenzker, L.
History
DepositionAug 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Mar 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)42,7466
Polymers42,1691
Non-polymers5775
Water1,820101
1
A: Farnesyl pyrophosphate synthase
hetero molecules

A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,49212
Polymers84,3382
Non-polymers1,15310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area7480 Å2
ΔGint-94 kcal/mol
Surface area27420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.583, 60.583, 341.208
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-529-

HOH

21A-567-

HOH

31A-591-

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, 106 molecules

#2: Chemical ChemComp-PKD / (4S)-3-(4-chlorobenzene-1-carbonyl)-1,3-thiazolidine-4-carboxylic acid


Mass: 271.720 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H10ClNO3S
#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.: 101 / 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: 2.14 Å3/Da / Density % sol: 42.61 % / Mosaicity: 0.05 °
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: 0.9677 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.072→56.868 Å / Num. obs: 17265 / % possible obs: 72.3 % / Redundancy: 36.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.343 / Rpim(I) all: 0.052 / Rrim(I) all: 0.322 / Rsym value: 0.343 / Net I/σ(I): 14.6 / Num. measured all: 586997 / Scaling rejects: 3
Reflection shellResolution: 2.072→2.257 Å / Redundancy: 23.4 % / Rmerge(I) obs: 2.733 / Mean I/σ(I) obs: 1.6 / Num. measured all: 87927 / Num. unique obs: 2175 / CC1/2: 0.872 / Rpim(I) all: 0.397 / Rrim(I) all: 2.549 / Rsym value: 2.733 / Net I/σ(I) obs: 2.4 / % possible all: 16.6

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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: 2.072→56.868 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2826 851 4.93 %
Rwork0.2533 16409 -
obs0.2548 17260 72.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.45 Å2 / Biso mean: 44.5737 Å2 / Biso min: 8.28 Å2
Refinement stepCycle: final / Resolution: 2.072→56.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2619 0 34 101 2754
Biso mean--69.39 42.21 -
Num. residues----329
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0725-2.20230.3319200.310644246212
2.2023-2.37240.3329710.29331419149039
2.3724-2.61110.31491470.29122890303778
2.6111-2.9890.28751940.28537433937100
2.989-3.76570.30332020.255838214023100
3.7657-56.88940.25112170.220440944311100

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