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- PDB-5qtk: T. brucei FPPS in complex with CID 69539 -

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Basic information

Entry
Database: PDB / ID: 5qtk
TitleT. brucei FPPS in complex with CID 69539
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
N,N-diethyl-4-methylbenzene-1-sulfonamide / PHOSPHATE ION / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.857 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 69539
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)42,6095
Polymers42,1691
Non-polymers4404
Water2,360131
1
A: Farnesyl pyrophosphate synthase
hetero molecules

A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,21910
Polymers84,3382
Non-polymers8818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area6900 Å2
ΔGint-89 kcal/mol
Surface area27680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.526, 60.526, 340.841
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-524-

HOH

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Components

#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
#2: Chemical ChemComp-PJP / N,N-diethyl-4-methylbenzene-1-sulfonamide


Mass: 227.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17NO2S
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 42.44 % / 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: ID30B / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 1.857→56.807 Å / Num. obs: 22050 / % possible obs: 67.4 % / Redundancy: 35.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.296 / Rpim(I) all: 0.047 / Rrim(I) all: 0.277 / Rsym value: 0.296 / Net I/σ(I): 14.3 / Num. measured all: 725619 / Scaling rejects: 5
Reflection shellResolution: 1.857→2.057 Å / Redundancy: 30.9 % / Rmerge(I) obs: 3.265 / Mean I/σ(I) obs: 1.6 / Num. measured all: 104606 / Num. unique obs: 2852 / CC1/2: 0.929 / Rpim(I) all: 0.473 / Rrim(I) all: 2.89 / Rsym value: 3.265 / Net I/σ(I) obs: 2.3 / % possible all: 13.1

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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: 1.857→56.807 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.29 1090 4.94 %
Rwork0.2512 20959 -
obs0.2532 22049 67.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.68 Å2 / Biso mean: 38.3209 Å2 / Biso min: 3.5 Å2
Refinement stepCycle: final / Resolution: 1.857→56.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2629 0 26 131 2786
Biso mean--72.09 42.49 -
Num. residues----330
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8574-1.94190.2372160.39771561724
1.9419-2.04430.3466280.31675578320
2.0443-2.17240.3507820.29971683176544
2.1724-2.34020.30581270.28392511263866
2.3402-2.57570.32822040.28583750395498
2.5757-2.94830.30221990.273438854084100
2.9483-3.71450.29022090.242539644173100
3.7145-56.83340.26032250.218542554480100

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