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- PDB-4rxd: T. Brucei Farnesyl Diphosphate Synthase Complexed with Risedronate -

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Basic information

Entry
Database: PDB / ID: 4rxd
TitleT. Brucei Farnesyl Diphosphate Synthase Complexed with Risedronate
ComponentsFarnesyl pyrophosphate synthase
KeywordsTRANSFERASE
Function / homology
Function and homology information


prenyltransferase activity / isoprenoid biosynthetic process / 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
Chem-RIS / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCao, R. / Liu, Y.-L. / Oldfield, E.
CitationJournal: ACS Med Chem Lett / Year: 2015
Title: Farnesyl diphosphate synthase inhibitors with unique ligand-binding geometries.
Authors: Liu, Y.L. / Cao, R. / Wang, Y. / Oldfield, E.
History
DepositionDec 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Structure summary / Item: _chem_comp.pdbx_synonyms
Revision 1.2Sep 20, 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_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_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_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

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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)134,49515
Polymers133,4273
Non-polymers1,06812
Water8,719484
1
A: Farnesyl pyrophosphate synthase
C: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,66410
Polymers88,9512
Non-polymers7128
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8060 Å2
ΔGint-91 kcal/mol
Surface area26680 Å2
MethodPISA
2
B: Farnesyl pyrophosphate synthase
hetero molecules

B: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,66410
Polymers88,9512
Non-polymers7128
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area8030 Å2
ΔGint-92 kcal/mol
Surface area26890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.340, 90.305, 88.709
Angle α, β, γ (deg.)90.000, 89.910, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1732-

HOH

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Components

#1: Protein Farnesyl pyrophosphate synthase


Mass: 44475.738 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q86C09
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-RIS / 1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID / Risedronate


Mass: 283.112 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H11NO7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.35 Å3/Da / Density % sol: 47.58 %
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: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 28, 2008
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 82972 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2→2.07 Å / % possible all: 99.2

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.15data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OGD

2ogd


Resolution: 2→29.55 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.137 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2508 4142 5 %RANDOM
Rwork0.2112 ---
obs0.2132 78824 99.69 %-
all-82966 --
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 max: 84.9 Å2 / Biso mean: 28.582 Å2 / Biso min: 10.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20.08 Å2
2--0 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8547 0 60 484 9091
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228789
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.97211901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.48951064
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.09824.074405
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.396151545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5371554
X-RAY DIFFRACTIONr_chiral_restr0.0870.21317
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026587
X-RAY DIFFRACTIONr_nbd_refined0.2080.24508
X-RAY DIFFRACTIONr_nbtor_refined0.3020.26170
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2552
X-RAY DIFFRACTIONr_metal_ion_refined0.0090.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.2239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.251
X-RAY DIFFRACTIONr_mcbond_it0.7211.55515
X-RAY DIFFRACTIONr_mcangle_it1.15228598
X-RAY DIFFRACTIONr_scbond_it1.70933787
X-RAY DIFFRACTIONr_scangle_it2.5964.53303
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 311 -
Rwork0.237 5654 -
all-5965 -
obs--97.31 %

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