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- PDB-1yhm: Structure of the complex of Trypanosoma cruzi farnesyl disphospha... -

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Basic information

Entry
Database: PDB / ID: 1yhm
TitleStructure of the complex of Trypanosoma cruzi farnesyl disphosphate synthase with alendronate, Isopentenyl diphosphate and mg+2
Componentsfarnesyl pyrophosphate synthaseDimethylallyltranstransferase
KeywordsTRANSFERASE / farnesyl diphosphate synthase / alendronate / isopentenyl diphosphate / mevalonate patway / geranyl transferase / dimethylallyl transferase / FPPS
Function / homology
Function and homology information


transferase activity, transferring alkyl or aryl (other than methyl) groups / isoprenoid biosynthetic process / membrane / 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
4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDIPHOSPHONATE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / Farnesyl diphosphate synthase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGabelli, S.B. / McLellan, J.S. / Montalvetti, A. / Oldfield, E. / Docampo, R. / Amzel, L.M.
CitationJournal: Proteins / Year: 2005
Title: Structure and mechanism of the farnesyl diphosphate synthase from Trypanosoma cruzi: Implications for drug design.
Authors: Gabelli, S.B. / McLellan, J.S. / Montalvetti, A. / Oldfield, E. / Docampo, R. / Amzel, L.M.
History
DepositionJan 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 17, 2013Group: Non-polymer description
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / 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: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)127,76721
Polymers125,7863
Non-polymers1,98018
Water1,982110
1
A: farnesyl pyrophosphate synthase
B: farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,17814
Polymers83,8572
Non-polymers1,32012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9360 Å2
ΔGint-93 kcal/mol
Surface area26860 Å2
MethodPISA
2
C: farnesyl pyrophosphate synthase
hetero molecules

C: farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,17814
Polymers83,8572
Non-polymers1,32012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556x-y,-y,-z+11
Unit cell
Length a, b, c (Å)103.205, 103.205, 385.236
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThe biological assembly is a dimer, in this case formed by monomers A and B.

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein farnesyl pyrophosphate synthase / Dimethylallyltranstransferase


Mass: 41928.746 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: TcFPPS / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: UniProt: Q8WS26, (2E,6E)-farnesyl diphosphate synthase

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Non-polymers , 5 types, 128 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-AHD / 4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDIPHOSPHONATE / ALENDRONATE / FOSAMAX (TM) / Alendronic acid


Mass: 245.064 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H9NO7P2 / Comment: medication*YM
#5: Chemical ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE / Isopentenyl pyrophosphate


Mass: 246.092 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H12O7P2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 48.3 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 4.6
Details: peg 4000 Na acetate amonium sulfate, pH 4.6, LIQUID DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 16, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→87.71 Å / Num. obs: 55148 / Redundancy: 12.9 % / Rmerge(I) obs: 0.146
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.895 / % possible all: 95.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.501data extraction
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YHK

1yhk


Resolution: 2.5→87.71 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.906 / SU B: 10.981 / SU ML: 0.24 / Cross valid method: THROUGHOUT / ESU R: 0.677 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2777 2189 5.1 %RANDOM
Rwork0.20798 ---
obs0.2114 40998 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.193 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20.75 Å20 Å2
2--1.5 Å20 Å2
3----2.26 Å2
Refinement stepCycle: LAST / Resolution: 2.5→87.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8673 0 108 110 8891
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0228958
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9811.96312150
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0651083
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.89724.307411
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.417151539
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6921545
X-RAY DIFFRACTIONr_chiral_restr0.1820.21335
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026696
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.250.24993
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.26313
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2453
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1530.219
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.2108
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1040.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5091.55543
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.39728736
X-RAY DIFFRACTIONr_scbond_it2.9133877
X-RAY DIFFRACTIONr_scangle_it3.934.53414
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 159 -
Rwork0.297 2957 -
obs--99.97 %

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