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- PDB-3wca: The complex structure of TcSQS with ligand, FSPP -

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Basic information

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


squalene synthase / farnesyl-diphosphate farnesyltransferase activity / squalene synthase activity / lipid biosynthetic process / membrane
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. / Squalene/phytoene synthase / Trans-isoprenyl diphosphate synthases, head-to-head / 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. / Squalene/phytoene synthase / Trans-isoprenyl diphosphate synthases, head-to-head / Squalene/phytoene synthase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-FPS / Squalene synthase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsShang, N. / Li, Q. / Ko, T.P. / Chan, H.C. / Huang, C.H. / Oldfield, E. / 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 26, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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)169,51212
Polymers167,4474
Non-polymers2,0658
Water13,349741
1
A: Farnesyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2853
Polymers41,8621
Non-polymers4232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Farnesyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3094
Polymers41,8621
Non-polymers4473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Farnesyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6593
Polymers41,8621
Non-polymers7972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Farnesyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2602
Polymers41,8621
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.129, 132.869, 141.915
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 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RP / 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.: 5 / Source method: obtained synthetically / Formula: C15H28O6P2S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 741 / 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: 2.23 Å3/Da / Density % sol: 44.78 %
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: 2.24→25 Å / Num. obs: 72859 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 44.6
Reflection shellResolution: 2.24→2.32 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 5.4 / Num. unique all: 7185 / % possible all: 100

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Processing

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

1ezf


Resolution: 2.24→25 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.259 3592 RANDOM
Rwork0.215 --
all-72569 -
obs-70721 -
Refinement stepCycle: LAST / Resolution: 2.24→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11005 0 123 741 11869
LS refinement shellResolution: 2.24→2.32 Å
RfactorNum. reflection
Rfree0.311 322
Rwork0.266 -
obs-6618

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