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- PDB-3wcb: The complex structure of TcSQS with ligand, BPH1237 -

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Basic information

Entry
Database: PDB / ID: 3wcb
TitleThe complex structure of TcSQS with ligand, BPH1237
ComponentsFarnesyltransferase, putative
KeywordsTRANSFERASE / isoprenoids / drug discovery / Trypanosoma cruzi squalene synthase / BPH-1237
Function / homology
Function and homology information


squalene synthase / squalene synthase [NAD(P)H] activity / : / farnesyltranstransferase activity / lipid biosynthetic process / 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-8PH / Squalene synthase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsShang, N. / Li, Q. / Ko, T.P. / Chan, H.C. / Huang, C.H. / Ren, F. / Zheng, Y. / Zhu, Z. / Chen, C.C. / Guo, R.T.
CitationJournal: Plos Pathog. / Year: 2014
Title: Squalene synthase as a target for Chagas disease therapeutics.
Authors: Shang, N. / Li, Q. / Ko, T.P. / Chan, H.C. / Li, J. / Zheng, Y. / Huang, C.H. / Ren, F. / Chen, C.C. / Zhu, Z. / Galizzi, M. / Li, Z.H. / Rodrigues-Poveda, C.A. / Gonzalez-Pacanowska, D. / ...Authors: Shang, N. / Li, Q. / Ko, T.P. / Chan, H.C. / Li, J. / Zheng, Y. / Huang, C.H. / Ren, F. / Chen, C.C. / Zhu, Z. / Galizzi, M. / Li, Z.H. / Rodrigues-Poveda, C.A. / Gonzalez-Pacanowska, D. / Veiga-Santos, P. / de Carvalho, T.M. / de Souza, W. / Urbina, J.A. / Wang, A.H. / Docampo, R. / Li, K. / Liu, Y.L. / Oldfield, E. / Guo, R.T.
History
DepositionMay 27, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 18, 2014Provider: 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

Downloads & links

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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)169,2178
Polymers167,5674
Non-polymers1,6494
Water3,531196
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)42,3042
Polymers41,8921
Non-polymers4121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Farnesyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3042
Polymers41,8921
Non-polymers4121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Farnesyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3042
Polymers41,8921
Non-polymers4121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: Farnesyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3042
Polymers41,8921
Non-polymers4121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.395, 127.694, 142.562
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: 41891.832 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 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RP / References: UniProt: Q4CWB4, squalene synthase
#2: Chemical
ChemComp-8PH / hydrogen [(1R)-2-(3-decyl-1H-imidazol-3-ium-1-yl)-1-hydroxy-1-phosphonoethyl]phosphonate


Mass: 412.355 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H30N2O7P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.16 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris, 21% PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 3→25 Å / Num. obs: 29564 / % possible obs: 99.1 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 15.1
Reflection shellResolution: 3→3.11 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 1.6 / Num. unique all: 2752 / % possible all: 94.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EZF

1ezf


Resolution: 3→25 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.252 1351 RANDOM
Rwork0.198 --
all-29653 -
obs-27727 -
Refinement stepCycle: LAST / Resolution: 3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11013 0 64 196 11273
LS refinement shellResolution: 3→3.11 Å / Rfactor Rfree: 0.363 / Rfactor Rwork: 0.324

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