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- PDB-3wsb: The Tuberculosis Drug SQ109 Inhibits Trypanosoma cruzi Cell Proli... -

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Basic information

Entry
Database: PDB / ID: 3wsb
TitleThe Tuberculosis Drug SQ109 Inhibits Trypanosoma cruzi Cell Proliferation and acts Synergistically with Posaconazole
ComponentsFarnesyltransferase, putative
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / isoprenoids / drug discovery / Trypanosoma cruzi squalene synthase / SQ109 / FSPP / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


squalene synthase / farnesyl diphosphate metabolic process / squalene synthase [NAD(P)H] activity / lipid biosynthetic process / endoplasmic reticulum membrane / metal ion binding
Similarity search - Function
Squalene synthase-like / Trans-isoprenyl diphosphate synthases, eukaryotic-type / Squalene and phytoene synthases signature 2. / Squalene/phytoene synthase, conserved site / Squalene and phytoene synthases signature 1. / Trans-isoprenyl diphosphate synthases, head-to-head / Squalene/phytoene synthase / Squalene/phytoene synthase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase ...Squalene synthase-like / Trans-isoprenyl diphosphate synthases, eukaryotic-type / Squalene and phytoene synthases signature 2. / Squalene/phytoene synthase, conserved site / Squalene and phytoene synthases signature 1. / Trans-isoprenyl diphosphate synthases, head-to-head / Squalene/phytoene synthase / Squalene/phytoene synthase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-FPS / Chem-RWZ / Squalene synthase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsShang, N. / Li, Q. / Huang, C.H. / Oldfield, E. / Guo, R.T.
CitationJournal: To be Published
Title: The Tuberculosis Drug SQ109 Inhibits Trypanosoma cruzi Cell Proliferation and acts Synergistically with Posaconazole
Authors: Shang, N. / Li, Q. / Huang, C.H. / Oldfield, E. / Guo, R.T.
History
DepositionMar 5, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Farnesyltransferase, putative
B: Farnesyltransferase, putative
C: Farnesyltransferase, putative
D: Farnesyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,36312
Polymers167,4474
Non-polymers2,9168
Water7,800433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Farnesyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5913
Polymers41,8621
Non-polymers7292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Farnesyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5913
Polymers41,8621
Non-polymers7292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Farnesyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5913
Polymers41,8621
Non-polymers7292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: Farnesyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5913
Polymers41,8621
Non-polymers7292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.361, 130.566, 144.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Farnesyltransferase, putative


Mass: 41861.809 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 25-368 / Mutation: D82E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: CL Brener / Gene: Tc00.1047053508369.20 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4CWB4, squalene synthase
#2: Chemical
ChemComp-FPS / S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE / FARNESYL THIOPYROPHOSPHATE


Mass: 398.392 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H28O6P2S
#3: Chemical
ChemComp-RWZ / N-[(2Z)-3,7-dimethylocta-2,6-dien-1-yl]-N'-[(1R,3S,5R,7R)-tricyclo[3.3.1.1~3,7~]dec-2-yl]ethane-1,2-diamine


Mass: 330.551 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H38N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris, pH 8.5, 21% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→25 Å / Num. obs: 57874 / % possible obs: 97.1 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 26.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2.3 / Num. unique all: 25911 / % possible all: 90

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EZF

1ezf


Resolution: 2.4→24.9 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.277 2761 RANDOM
Rwork0.216 --
all-59431 -
obs-54530 -
Refinement stepCycle: LAST / Resolution: 2.4→24.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11005 0 192 433 11630
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree: 0.341 / Rfactor Rwork: 0.296

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