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- PDB-4jzx: Crystal Structure of Leshmaniasis major Farnesyl diphosphate synt... -

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Basic information

Entry
Database: PDB / ID: 4jzx
TitleCrystal Structure of Leshmaniasis major Farnesyl diphosphate synthase in complex with 3-BUTYL-1-(2,2-DIPHOSPHONOETHYL)PYRIDINIUM, IPP and Ca2+
ComponentsFarnesyl pyrophosphate synthaseDimethylallyltranstransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Geranyl Transferase / FPPS / farnesyl pyrophosphate synthase / farnesyl diphosphate synthase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / dimethylallyltranstransferase 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-butyl-1-(2,2-diphosphonoethyl)pyridinium / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsAripirala, S. / Gabelli, S. / Amzel, L.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural and thermodynamic basis of the inhibition of Leishmania major farnesyl diphosphate synthase by nitrogen-containing bisphosphonates.
Authors: Aripirala, S. / Gonzalez-Pacanowska, D. / Oldfield, E. / Kaiser, M. / Amzel, L.M. / Gabelli, S.B.
History
DepositionApr 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,47212
Polymers82,0902
Non-polymers1,38110
Water13,980776
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7530 Å2
ΔGint-112 kcal/mol
Surface area27430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.428, 85.805, 106.867
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Farnesyl pyrophosphate synthase / Dimethylallyltranstransferase


Mass: 41045.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: FPPS, LMJF_22_1360 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q4QBL1, dimethylallyltranstransferase, (2E,6E)-farnesyl diphosphate synthase
#2: Chemical ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE / Isopentenyl pyrophosphate


Mass: 246.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O7P2
#3: Chemical ChemComp-476 / 3-butyl-1-(2,2-diphosphonoethyl)pyridinium


Mass: 324.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H20NO6P2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 776 / 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: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 291 K / Method: hanging drop / pH: 6.5 / Details: PEG 3350, pH 6.5, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: May 20, 2009
RadiationMonochromator: Varimax mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 68699 / % possible obs: 99.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.07 / Χ2: 1.485 / Net I/σ(I): 10.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.865.40.54567880.686199.9
1.86-1.946.90.41367820.7541100
1.94-2.036.90.29668060.9111100
2.03-2.136.90.20668141.1071100
2.13-2.2770.15968201.3011100
2.27-2.4470.12568421.5611100
2.44-2.6970.168631.696199.9
2.69-3.087.10.07368751.949199.9
3.08-3.887.10.05569552.328199.7
3.88-5070.04371542.23198.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→25.94 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.2166 / WRfactor Rwork: 0.1701 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8392 / SU B: 2.504 / SU ML: 0.08 / SU R Cruickshank DPI: 0.1363 / SU Rfree: 0.1335 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 3477 5.1 %RANDOM
Rwork0.1782 ---
obs0.1807 68610 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 88.22 Å2 / Biso mean: 28.0746 Å2 / Biso min: 18.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20 Å2
2---0.56 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5752 0 74 776 6602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226026
X-RAY DIFFRACTIONr_angle_refined_deg1.1081.9618190
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2865744
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.66924.522272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.363151038
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4211526
X-RAY DIFFRACTIONr_chiral_restr0.0750.2913
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024504
X-RAY DIFFRACTIONr_nbd_refined0.1950.23360
X-RAY DIFFRACTIONr_nbtor_refined0.30.24235
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2722
X-RAY DIFFRACTIONr_metal_ion_refined0.120.231
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1340.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.233
X-RAY DIFFRACTIONr_mcbond_it0.5561.53762
X-RAY DIFFRACTIONr_mcangle_it0.85825896
X-RAY DIFFRACTIONr_scbond_it1.47232600
X-RAY DIFFRACTIONr_scangle_it2.3174.52287
LS refinement shellResolution: 1.803→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 223 -
Rwork0.275 4712 -
all-4935 -
obs--99.02 %

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