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- PDB-5ael: T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphospho... -

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Basic information

Entry
Database: PDB / ID: 5ael
TitleT. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-597
ComponentsFARNESYL PYROPHOSPHATE SYNTHASE
KeywordsTRANSFERASE
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-QAF / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYang, G. / Oldfield, E. / No, J.H.
Citation
Journal: Antimicrob.Agents Chemother. / Year: 2015
Title: Inhibition of Trypanosoma Brucei Cell Growth by Lipophilic Bisphosphonates: An in Vitro and in Vivo Investigation.
Authors: Yang, G. / Zhu, W. / Kim, K. / Byun, S.Y. / Choi, G. / Wang, K. / Cha, J.S. / Cho, H. / Oldfield, E. / No, J.H.
#1: Journal: Proteins / Year: 2008
Title: Structures of a Potent Phenylalkyl Bisphosphonate Inhibitor Bound to Farnesyl and Geranylgeranyl Diphosphate Synthases.
Authors: Cao, R. / Chen, C.K. / Guo, R. / Wang, A.H. / Oldfield, E.
History
DepositionDec 26, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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_conn.ptnr2_label_seq_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
B: FARNESYL PYROPHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,86410
Polymers84,0302
Non-polymers8348
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-80.1 kcal/mol
Surface area27350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.835, 118.250, 62.424
Angle α, β, γ (deg.)90.00, 112.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein FARNESYL PYROPHOSPHATE SYNTHASE


Mass: 42015.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI (eukaryote) / Production host: ESCHERICHIA COLI BL21 (bacteria)
References: UniProt: Q86C09, (2E,6E)-farnesyl diphosphate synthase
#2: Chemical ChemComp-QAF / {2-[3-(hex-1-yn-1-yl)pyridinium-1-yl]ethane-1,1-diyl}bis(phosphonate)


Mass: 344.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H16NO6P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.72 Å3/Da / Density % sol: 54.76 % / Description: NONE
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.75
Details: 6% MPD, 0.1 AMMONIUM ACETATE, PH 5.75, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→85.49 Å / Num. obs: 25663 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.8
Reflection shellResolution: 2.61→2.66 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 16.8 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P1C

2p1c


Resolution: 2.6→85.49 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.928 / SU B: 9.819 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.808 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22957 1362 5 %RANDOM
Rwork0.16376 ---
obs0.16712 25663 97.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.813 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.02 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.6→85.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5708 0 50 220 5978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195870
X-RAY DIFFRACTIONr_bond_other_d0.0040.025532
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.9737944
X-RAY DIFFRACTIONr_angle_other_deg0.826312728
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3975710
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.99424.074270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.44151030
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9391536
X-RAY DIFFRACTIONr_chiral_restr0.080.2876
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026548
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021334
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4144.922852
X-RAY DIFFRACTIONr_mcbond_other3.4144.9182851
X-RAY DIFFRACTIONr_mcangle_it5.097.3593558
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.3045.373018
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.598→2.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 96 -
Rwork0.221 1506 -
obs--78.03 %

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