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- PDB-4e1e: Crystal structure of Trypanosome cruzi farnesyl diphosphate synth... -

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Basic information

Entry
Database: PDB / ID: 4e1e
TitleCrystal structure of Trypanosome cruzi farnesyl diphosphate synthase in complex with [2-(n-hexylamino)ethane-1,1-diyl]bisphosphonic acid and Mg2+
ComponentsFarnesyl pyrophosphate synthase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / geranyl transferase / farnesyl pyrophosphate synthase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / metal ion binding / cytoplasm
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-0MW / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.65 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
DepositionMar 6, 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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)41,7257
Polymers41,0941
Non-polymers6316
Water41423
1
A: Farnesyl pyrophosphate synthase
hetero molecules

A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,45114
Polymers82,1882
Non-polymers1,26212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area7800 Å2
ΔGint-76 kcal/mol
Surface area27180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.575, 58.575, 393.933
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 41094.133 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 , 5 types, 29 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 289.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H21NO6P2
#4: Chemical ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE


Mass: 246.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O7P2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.37 Å3/Da / Density % sol: 48.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG4000, pH 5.0, 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: Nov 11, 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: 2.65→65.656 Å / Num. obs: 12287 / % possible obs: 95.7 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.105 / Χ2: 2.266 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.65-2.713.60.4736121.576199.8
2.7-2.7415.60.4366081.6651100
2.74-2.815.50.3726121.7161100
2.8-2.8515.40.3465981.73199.8
2.85-2.9215.60.2726391.882199.7
2.92-2.9815.30.2356102.0331100
2.98-3.0615.60.2096152.008199.8
3.06-3.1415.40.1866102.193199.8
3.14-3.2315.40.1696442.207199.4
3.23-3.3415.30.1416012.413199.5
3.34-3.4615.20.1186432.451199.8
3.46-3.6150.1126102.537199.2
3.6-3.7613.20.1186143.279195.6
3.76-3.96140.0876402.719199.5
3.96-4.213.30.0836103.01192.8
4.2-4.5312.60.0745832.838190.8
4.53-4.9811.30.0675942.665190.1
4.98-5.713.20.0636592.387198.2
5.7-7.1613.80.0586872.278198
7.16-309.10.054982.191161.6

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Processing

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

4dwg


Resolution: 2.65→28.969 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.838 / WRfactor Rfree: 0.3 / WRfactor Rwork: 0.2219 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7924 / SU B: 15.014 / SU ML: 0.315 / SU Rfree: 0.4277 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.428 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3082 587 4.8 %RANDOM
Rwork0.2317 ---
obs0.2351 12120 95.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 75.94 Å2 / Biso mean: 51.3117 Å2 / Biso min: 16.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20.34 Å20 Å2
2--0.68 Å20 Å2
3----1.01 Å2
Refinement stepCycle: LAST / Resolution: 2.65→28.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2883 0 35 23 2941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222999
X-RAY DIFFRACTIONr_angle_refined_deg1.1331.9594068
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6655364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.52624.317139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73715513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.181515
X-RAY DIFFRACTIONr_chiral_restr0.0770.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212254
X-RAY DIFFRACTIONr_mcbond_it0.3831.51811
X-RAY DIFFRACTIONr_mcangle_it0.72822926
X-RAY DIFFRACTIONr_scbond_it0.96231188
X-RAY DIFFRACTIONr_scangle_it1.6224.51142
LS refinement shellResolution: 2.65→2.792 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.377 104 -
Rwork0.294 1651 -
all-1755 -
obs--98.54 %

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