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

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Basic information

Entry
Database: PDB / ID: 4dxj
TitleCrystal structure of Trypanosome cruzi farnesyl diphosphate synthase in complex with [2-(n-propylamino)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-0M9 / ACETATE ION / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.35 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 27, 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_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_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
B: Farnesyl pyrophosphate synthase
C: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,30627
Polymers123,6763
Non-polymers2,63024
Water2,900161
1
A: Farnesyl pyrophosphate synthase
B: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,24418
Polymers82,4512
Non-polymers1,79316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9470 Å2
ΔGint-84 kcal/mol
Surface area27230 Å2
MethodPISA
2
C: Farnesyl pyrophosphate synthase
hetero molecules

C: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,12518
Polymers82,4512
Non-polymers1,67516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556x-y,-y,-z+11
Buried area9180 Å2
ΔGint-64 kcal/mol
Surface area27250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.220, 103.220, 386.658
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, 3 molecules ABC

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


Mass: 41225.324 Da / Num. of mol.: 3
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 , 8 types, 185 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-0M9 / [2-(propylamino)ethane-1,1-diyl]bis(phosphonic acid)


Mass: 247.123 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H15NO6P2
#4: Chemical ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE


Mass: 246.092 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H12O7P2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.4 Å3/Da / Density % sol: 48.83 %
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: Dec 6, 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: 2.35→89.391 Å / Num. obs: 49874 / % possible obs: 96 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.09 / Χ2: 1.241 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.35-2.396.80.5223460.649193.7
2.39-2.437.40.43424830.672198.7
2.43-2.488.70.45825570.6631100
2.48-2.539.80.41125250.7011100
2.53-2.599.80.33125450.7321100
2.59-2.659.90.29125390.761100
2.65-2.719.80.26425640.8081100
2.71-2.799.90.23625470.8431100
2.79-2.879.80.19225570.8991100
2.87-2.969.90.15525500.9881100
2.96-3.079.70.13425671.071100
3.07-3.199.80.11525751.121100
3.19-3.339.70.09325821.215199.8
3.33-3.519.50.08425711.38199.7
3.51-3.737.20.09111382.765143.7
3.73-4.028.20.07224211.833192.5
4.02-4.429.10.05926172.153199.1
4.42-5.0690.05726202.28198.4
5.06-6.379.20.05527231.917199.8
6.37-407.80.04328472.362196.3

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Processing

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

1yhm


Resolution: 2.35→38.722 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.9 / WRfactor Rfree: 0.2536 / WRfactor Rwork: 0.2 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8041 / SU B: 18.591 / SU ML: 0.203 / SU R Cruickshank DPI: 0.4888 / SU Rfree: 0.3046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.489 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2853 2519 5.1 %RANDOM
Rwork0.2195 ---
obs0.2228 49345 95.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 69.88 Å2 / Biso mean: 40.287 Å2 / Biso min: 14.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20.56 Å20 Å2
2--1.12 Å20 Å2
3----1.69 Å2
Refinement stepCycle: LAST / Resolution: 2.35→38.722 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8673 0 152 161 8986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0229029
X-RAY DIFFRACTIONr_angle_refined_deg1.2081.96512227
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.77351091
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.91624.296412
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.148151543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4561545
X-RAY DIFFRACTIONr_chiral_restr0.0890.21339
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216746
X-RAY DIFFRACTIONr_mcbond_it0.4041.55439
X-RAY DIFFRACTIONr_mcangle_it0.79328784
X-RAY DIFFRACTIONr_scbond_it1.34133590
X-RAY DIFFRACTIONr_scangle_it2.1314.53443
LS refinement shellResolution: 2.35→2.48 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.334 378 -
Rwork0.251 6754 -
all-7132 -
obs--97.01 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.34520.06920.21890.48750.14720.77660.04450.0194-0.12880.10930.04340.00120.10020.0064-0.08790.06340.0282-0.00390.0156-0.00090.054241.144249.1719204.0728
20.2369-0.0436-0.09960.34790.07710.5264-0.01260.03970.0585-0.00010.0647-0.0225-0.01290.0498-0.05210.02620.0010.01290.057-0.00830.036542.771370.2878180.7138
30.4516-0.0871-0.01860.4661-0.08980.8194-0.03540.03150.1491-0.0372-0.0513-0.0882-0.0389-0.04020.08660.0230.0104-0.01650.04030.00040.070344.890711.7761182.5297
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 362
2X-RAY DIFFRACTION1A401 - 405
3X-RAY DIFFRACTION2B1 - 362
4X-RAY DIFFRACTION2B401 - 405
5X-RAY DIFFRACTION3C1 - 362
6X-RAY DIFFRACTION3C401 - 405

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