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- PDB-5qti: T. brucei FPPS in complex with CID 62483448 -

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Basic information

Entry
Database: PDB / ID: 5qti
TitleT. brucei FPPS in complex with CID 62483448
ComponentsFarnesyl pyrophosphate synthaseDimethylallyltranstransferase
KeywordsTransferase/Transferase inhibitor / farnesyl diphosphate synthase / Trypanosoma brucei / PanDDA / protein-ligand complex / Transferase-Transferase inhibitor complex
Function / homology
Function and homology information


transferase activity, transferring alkyl or aryl (other than methyl) groups / isoprenoid biosynthetic process / metal ion binding
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
3-(2-bromophenoxy)pyridazine / PHOSPHATE ION / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.112 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 62483448
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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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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)42,7256
Polymers42,1691
Non-polymers5565
Water95553
1
A: Farnesyl pyrophosphate synthase
hetero molecules

A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,45112
Polymers84,3382
Non-polymers1,11210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area7520 Å2
ΔGint-93 kcal/mol
Surface area27350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.529, 60.529, 340.460
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-513-

HOH

21A-541-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Farnesyl pyrophosphate synthase / Dimethylallyltranstransferase


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, 58 molecules

#2: Chemical ChemComp-PJV / 3-(2-bromophenoxy)pyridazine


Mass: 251.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H7BrN2O
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.39 Å3/Da / Density % sol: 48.58 % / Mosaicity: 0.1 °
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-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.112→56.743 Å / Num. obs: 16042 / % possible obs: 70.2 % / Redundancy: 37.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.03 / Rrim(I) all: 0.187 / Rsym value: 0.198 / Net I/σ(I): 15.6 / Num. measured all: 545040
Reflection shellResolution: 2.112→2.315 Å / Redundancy: 26.2 % / Rmerge(I) obs: 2.231 / Mean I/σ(I) obs: 1.6 / Num. measured all: 83187 / Num. unique obs: 2024 / CC1/2: 0.93 / Rpim(I) all: 0.302 / Rrim(I) all: 1.953 / Rsym value: 2.231 / Net I/σ(I) obs: 2.5 / % possible all: 14.4

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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: 2.112→51.809 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2787 801 5 %
Rwork0.241 15234 -
obs0.243 16035 70.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.98 Å2 / Biso mean: 57.0449 Å2 / Biso min: 18.16 Å2
Refinement stepCycle: final / Resolution: 2.112→51.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2629 0 31 53 2713
Biso mean--82.01 54.05 -
Num. residues----330
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 (%)
2.112-2.23330.3287180.298933335110
2.2333-2.40570.2997590.29451054111330
2.4057-2.64780.30781400.28312699283976
2.6478-3.03090.28861880.269335893777100
3.0309-3.81840.28461900.247936393829100
3.8184-51.82490.2642060.215239204126100

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