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- PDB-5qtb: T. brucei FPPS in complex with CID 303798 -

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Basic information

Entry
Database: PDB / ID: 5qtb
TitleT. brucei FPPS in complex with CID 303798
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
DI(HYDROXYETHYL)ETHER / Chem-PJG / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.965 Å
AuthorsMuenzker, L. / Petrick, J.K. / Schleberger, C. / Jahnke, W.
CitationJournal: To Be Published
Title: T. brucei FPPS in complex with CID 303798
Authors: Muenzker, L.
History
DepositionAug 7, 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)42,5484
Polymers42,1691
Non-polymers3793
Water1,51384
1
A: Farnesyl pyrophosphate synthase
hetero molecules

A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,0968
Polymers84,3382
Non-polymers7576
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area6300 Å2
ΔGint-22 kcal/mol
Surface area27480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.961, 60.961, 340.711
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-519-

HOH

21A-537-

HOH

31A-548-

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-PJG / N~1~-[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]decan-1-yl]ethane-1,2-diamine


Mass: 194.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H22N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.17 Å3/Da / Density % sol: 43.24 % / Mosaicity: 0.08 °
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: SLS / Beamline: X10SA / Wavelength: 0.99993 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99993 Å / Relative weight: 1
ReflectionResolution: 1.965→52.794 Å / Num. obs: 17981 / % possible obs: 63.9 % / Redundancy: 18.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.044 / Rrim(I) all: 0.189 / Rsym value: 0.139 / Net I/σ(I): 17.8 / Num. measured all: 436762
Reflection shellResolution: 1.965→2.112 Å / Redundancy: 18.9 % / Rmerge(I) obs: 2.454 / Mean I/σ(I) obs: 1.5 / Num. measured all: 71436 / Num. unique obs: 3623 / CC1/2: 0.48 / Rpim(I) all: 1.279 / Rrim(I) all: 5.711 / Rsym value: 2.454 / Net I/σ(I) obs: 0.7 / % possible all: 17

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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: 1.965→52.794 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2718 883 4.91 %
Rwork0.2289 17092 -
obs0.231 17975 63.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.29 Å2 / Biso mean: 48.5156 Å2 / Biso min: 7.56 Å2
Refinement stepCycle: final / Resolution: 1.965→52.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2595 0 25 84 2704
Biso mean--65.88 46.45 -
Num. residues----325
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 (%)
1.9653-2.08840.3014300.30467970916
2.0884-2.24970.323720.28421335140733
2.2497-2.47610.30581440.2822917306169
2.4761-2.83440.31561780.26373408358677
2.8344-3.57090.2862210.24134204442593
3.5709-52.81280.23922380.19494549478794

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