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- PDB-3dyh: T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphospho... -

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Basic information

Entry
Database: PDB / ID: 3dyh
TitleT. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-721
ComponentsFarnesyl pyrophosphate synthase
KeywordsTRANSFERASE / PROTEIN-BISPHOSPHONATE COMPLEX / Isoprene biosynthesis
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
3-butoxy-1-(2,2-diphosphonoethyl)pyridinium / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsCao, R. / Gao, Y. / Robinson, H. / Goddard, A. / Oldfield, E.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Lipophilic bisphosphonates as dual farnesyl/geranylgeranyl diphosphate synthase inhibitors: an X-ray and NMR investigation.
Authors: Zhang, Y. / Cao, R. / Yin, F. / Hudock, M.P. / Guo, R.T. / Krysiak, K. / Mukherjee, S. / Gao, Y.G. / Robinson, H. / Song, Y. / No, J.H. / Bergan, K. / Leon, A. / Cass, L. / Goddard, A. / ...Authors: Zhang, Y. / Cao, R. / Yin, F. / Hudock, M.P. / Guo, R.T. / Krysiak, K. / Mukherjee, S. / Gao, Y.G. / Robinson, H. / Song, Y. / No, J.H. / Bergan, K. / Leon, A. / Cass, L. / Goddard, A. / Chang, T.K. / Lin, F.Y. / Van Beek, E. / Papapoulos, S. / Wang, A.H. / Kubo, T. / Ochi, M. / Mukkamala, D. / Oldfield, E.
History
DepositionJul 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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_ref_seq_dif.details / _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
B: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,77810
Polymers88,9512
Non-polymers8268
Water6,287349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-100 kcal/mol
Surface area27130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.915, 118.733, 63.036
Angle α, β, γ (deg.)90.00, 112.29, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Farnesyl pyrophosphate synthase


Mass: 44475.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q86C09, (2E,6E)-farnesyl diphosphate synthase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-721 / 3-butoxy-1-(2,2-diphosphonoethyl)pyridinium


Mass: 340.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H20NO7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.61 Å3/Da / Density % sol: 52.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.75
Details: 10% MPD, 0.1 AMMONIUM ACETATE, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 123.2 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 22, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.94→30 Å / Num. obs: 65909 / % possible obs: 98.8 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 17.8
Reflection shellResolution: 1.94→2.02 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.509 / % possible all: 89.1

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→28.83 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.91 / SU B: 4.577 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28164 3331 5.1 %RANDOM
Rwork0.23952 ---
obs0.24164 62527 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.964 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.02 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.94→28.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5736 0 48 349 6133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225896
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.9747979
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6835713
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.43623.948271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.57151037
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9161538
X-RAY DIFFRACTIONr_chiral_restr0.0880.2883
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024414
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.23255
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24143
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2399
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0710.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.214
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7191.53692
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.14425758
X-RAY DIFFRACTIONr_scbond_it1.74532552
X-RAY DIFFRACTIONr_scangle_it2.6084.52221
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.94→1.992 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 230 -
Rwork0.307 3701 -
obs--79.93 %

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