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- PDB-4dwb: Crystal structure of Trypanosoma cruzi farnesyl diphosphate synth... -

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Basic information

Entry
Database: PDB / ID: 4dwb
TitleCrystal structure of Trypanosoma cruzi farnesyl diphosphate synthase in complex with [2-(n-pentylamino)ethane-1,1-diyl]bisphosphonic acid and Mg2+
ComponentsFarnesyl pyrophosphate synthaseDimethylallyltranstransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / geranyl transferase / 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 / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-0M7 / ACETATE ION / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsAripirala, S. / Amzel, L.M. / Gabelli, S.B.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Design, synthesis, calorimetry, and crystallographic analysis of 2-alkylaminoethyl-1,1-bisphosphonates as inhibitors of Trypanosoma cruzi farnesyl diphosphate synthase.
Authors: Aripirala, S. / Szajnman, S.H. / Jakoncic, J. / Rodriguez, J.B. / Docampo, R. / Gabelli, S.B. / Amzel, L.M.
History
DepositionFeb 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Non-polymer description
Revision 1.2Sep 13, 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_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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,09410
Polymers41,2251
Non-polymers8689
Water1,60389
1
A: Farnesyl pyrophosphate synthase
hetero molecules

A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,18720
Polymers82,4512
Non-polymers1,73718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area8950 Å2
ΔGint-150 kcal/mol
Surface area27740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.871, 57.871, 392.442
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-625-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Farnesyl pyrophosphate synthase / Dimethylallyltranstransferase / FPPS / farnesyl diphosphate synthase


Mass: 41225.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: FPPS / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q95WL3, (2E,6E)-farnesyl diphosphate synthase

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Non-polymers , 7 types, 98 molecules

#2: Chemical ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE / Isopentenyl pyrophosphate


Mass: 246.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O7P2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-0M7 / [2-(pentylamino)ethane-1,1-diyl]bis(phosphonic acid)


Mass: 275.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19NO6P2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 12.5 mg/mL protein in 250 uM inhibitor, 250 uM IPP, 1 mM magnesium chloride, mother liquor: 100 mM sodium acetate, pH 4.6-5.2, 200 mM ammonium sulfate, 2-10% PEG4000, VAPOR DIFFUSION, ...Details: 12.5 mg/mL protein in 250 uM inhibitor, 250 uM IPP, 1 mM magnesium chloride, mother liquor: 100 mM sodium acetate, pH 4.6-5.2, 200 mM ammonium sulfate, 2-10% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 2, 2011
RadiationMonochromator: Si(111) channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→65.407 Å / Num. obs: 22705 / % possible obs: 93.2 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.113 / Χ2: 1.793 / Net I/σ(I): 8.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.146.70.50911581.411198.2
2.14-2.177.40.42911361.422198.4
2.17-2.227.90.38611651.477198.5
2.22-2.2680.35511381.489198.4
2.26-2.318.10.31811801.55198.3
2.31-2.368.20.28911341.597198.2
2.36-2.428.20.24311921.616198.5
2.42-2.498.30.22211441.693198.1
2.49-2.568.30.20311641.753197.9
2.56-2.648.20.17211981.804197.7
2.64-2.748.30.15411481.816197
2.74-2.858.20.1411671.858197.6
2.85-2.988.10.11211601.94196.7
2.98-3.138.10.111831.991196.8
3.13-3.3380.08711682.022195.5
3.33-3.597.60.07811522.157192.2
3.59-3.946.80.06910952.14188.8
3.94-4.515.50.0639452.246174.3
4.51-5.665.60.0589792.135175
5.66-206.30.05710992.233175.4

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 4DWG

4dwg


Resolution: 2.1→19.891 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.877 / WRfactor Rfree: 0.2725 / WRfactor Rwork: 0.2118 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8425 / SU B: 5.534 / SU ML: 0.15 / SU R Cruickshank DPI: 0.2733 / SU Rfree: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.273 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2789 1156 5.1 %RANDOM
Rwork0.2178 ---
obs0.221 22545 92.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 75.85 Å2 / Biso mean: 31.5472 Å2 / Biso min: 8.59 Å2
Baniso -1Baniso -2Baniso -3
1-1.89 Å20.94 Å20 Å2
2--1.89 Å20 Å2
3----2.83 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2882 0 48 89 3019
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223007
X-RAY DIFFRACTIONr_angle_refined_deg1.7781.9654082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0035366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.75924.348138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.71215513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2691515
X-RAY DIFFRACTIONr_chiral_restr0.1130.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212260
X-RAY DIFFRACTIONr_mcbond_it11.51817
X-RAY DIFFRACTIONr_mcangle_it1.67822935
X-RAY DIFFRACTIONr_scbond_it331190
X-RAY DIFFRACTIONr_scangle_it4.3194.51146
LS refinement shellResolution: 2.1→2.152 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 81 -
Rwork0.24 1583 -
all-1664 -
obs--96.74 %

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