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

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Basic information

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


farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase 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-0M8 / ACETATE ION / DI(HYDROXYETHYL)ETHER / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.01 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 1.1Sep 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

Downloads & links

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Assembly

Deposited unit
A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,10112
Polymers41,2251
Non-polymers87511
Water4,414245
1
A: Farnesyl pyrophosphate synthase
hetero molecules

A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,20224
Polymers82,4512
Non-polymers1,75122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area8570 Å2
ΔGint-212 kcal/mol
Surface area27710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.173, 58.173, 391.822
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: 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, 256 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-0M8 / [2-(heptylamino)ethane-1,1-diyl]bis(phosphonic acid)


Mass: 303.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H23NO6P2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.32 Å3/Da / Density % sol: 47.01 %
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: Sep 30, 2010
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: 2.01→65.304 Å / Num. obs: 27252 / % possible obs: 97.8 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.08 / Χ2: 3.036 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.01-2.044.80.34612812.017198.7
2.04-2.085.50.31313821.844199.8
2.08-2.125.90.27113111.843199.8
2.12-2.176.60.25413682.0661100
2.17-2.217.20.22813342.833199.9
2.21-2.267.40.23213543.134199.7
2.26-2.327.30.19313482.474199.7
2.32-2.3870.17313392.812199.7
2.38-2.456.70.15613743.328199.6
2.45-2.536.50.14613833.398199.6
2.53-2.626.10.1313343.708199.6
2.62-2.735.60.11913713.603199.5
2.73-2.855.20.10713543.736198.5
2.85-34.40.09413665.306197.8
3-3.194.40.07113583.505197.3
3.19-3.444.10.06113603.272195.8
3.44-3.783.80.05213413.554195.4
3.78-4.333.70.04713433.529192.4
4.33-5.453.70.04213973.369193.7
5.45-5060.04315542.889191.8

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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 1YHL

1yhl


Resolution: 2.01→39.889 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.907 / WRfactor Rfree: 0.258 / WRfactor Rwork: 0.1936 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8212 / SU B: 5.335 / SU ML: 0.146 / SU R Cruickshank DPI: 0.2053 / SU Rfree: 0.1923 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1370 5 %RANDOM
Rwork0.202 ---
obs0.2053 27229 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 83.54 Å2 / Biso mean: 29.1704 Å2 / Biso min: 7.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20.3 Å20 Å2
2--0.59 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 2.01→39.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2882 0 49 245 3176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223006
X-RAY DIFFRACTIONr_angle_refined_deg1.8611.9634076
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4985366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02424.348138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.74215513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0041515
X-RAY DIFFRACTIONr_chiral_restr0.130.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212256
X-RAY DIFFRACTIONr_mcbond_it0.9881.51817
X-RAY DIFFRACTIONr_mcangle_it1.70522935
X-RAY DIFFRACTIONr_scbond_it3.08631189
X-RAY DIFFRACTIONr_scangle_it4.5054.51140
LS refinement shellResolution: 2.01→2.061 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 101 -
Rwork0.31 1813 -
all-1914 -
obs--97.8 %

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