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- PDB-5dgs: Crystal structure of human FPPS in complex with the monophosphona... -

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Basic information

Entry
Database: PDB / ID: 5dgs
TitleCrystal structure of human FPPS in complex with the monophosphonate compound 15
ComponentsFarnesyl pyrophosphate synthaseDimethylallyltranstransferase
KeywordsTRANSFERASE / ISOPRENE BIOSYNTHESIS / CHOLESTEROL BIOSYNTHESIS
Function / homology
Function and homology information


geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / Cholesterol biosynthesis / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / RNA binding ...geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / Cholesterol biosynthesis / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / RNA binding / nucleoplasm / metal ion binding / cytosol / 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-5A7 / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.62 Å
AuthorsRondeau, J.M. / Bourgier, E. / Lehmann, S.
Citation
#1: Journal: Nat.Chem.Biol. / Year: 2010
Title: Allosteric non-bisphosphonate FPPS inhibitors identified by fragment-based discovery.
Authors: Jahnke, W. / Rondeau, J.M. / Cotesta, S. / Marzinzik, A. / Pelle, X. / Geiser, M. / Strauss, A. / Gotte, M. / Bitsch, F. / Hemmig, R. / Henry, C. / Lehmann, S. / Glickman, J.F. / Roddy, T.P. ...Authors: Jahnke, W. / Rondeau, J.M. / Cotesta, S. / Marzinzik, A. / Pelle, X. / Geiser, M. / Strauss, A. / Gotte, M. / Bitsch, F. / Hemmig, R. / Henry, C. / Lehmann, S. / Glickman, J.F. / Roddy, T.P. / Stout, S.J. / Green, J.R.
#2: Journal: Chemmedchem / Year: 2015
Title: Discovery of Novel Allosteric Non-Bisphosphonate Inhibitors of Farnesyl Pyrophosphate Synthase by Integrated Lead Finding.
Authors: Marzinzik, A.L. / Amstutz, R. / Bold, G. / Bourgier, E. / Cotesta, S. / Glickman, J.F. / Gotte, M. / Henry, C. / Lehmann, S. / Hartwieg, J.C. / Ofner, S. / Pelle, X. / Roddy, T.P. / Rondeau, ...Authors: Marzinzik, A.L. / Amstutz, R. / Bold, G. / Bourgier, E. / Cotesta, S. / Glickman, J.F. / Gotte, M. / Henry, C. / Lehmann, S. / Hartwieg, J.C. / Ofner, S. / Pelle, X. / Roddy, T.P. / Rondeau, J.M. / Stauffer, F. / Stout, S.J. / Widmer, A. / Zimmermann, J. / Zoller, T. / Jahnke, W.
History
DepositionAug 28, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Nov 29, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
F: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6022
Polymers40,1841
Non-polymers4181
Water86548
1
F: Farnesyl pyrophosphate synthase
hetero molecules

F: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2044
Polymers80,3682
Non-polymers8372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4060 Å2
ΔGint-21 kcal/mol
Surface area29070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.962, 110.962, 74.772
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Farnesyl pyrophosphate synthase / Dimethylallyltranstransferase / FPS / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl ...FPS / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl diphosphate synthase / Geranyltranstransferase


Mass: 40183.855 Da / Num. of mol.: 1 / Fragment: UNP residues 72-419
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FDPS, FPS, KIAA1293 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): tuner
References: UniProt: P14324, (2E,6E)-farnesyl diphosphate synthase, dimethylallyltranstransferase
#2: Chemical ChemComp-5A7 / {(E)-2-[6-(acetylamino)-8-(naphthalen-1-yl)quinolin-2-yl]ethenyl}phosphonic acid


Mass: 418.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H19N2O4P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.86 Å3/Da / Density % sol: 57.05 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.7 / Details: 1.2M sodium potassium phosphate, 25% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Apr 18, 2007
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.62→78.46 Å / Num. obs: 14536 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13.8 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 17.84
Reflection shellResolution: 2.62→2.72 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 5.57 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSNovember 2005data reduction
SCALEPACKAugust 2005data scaling
CNX2002phasing
BUSTER-TNTBUSTER 2.11.2refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.62→23.17 Å / Cor.coef. Fo:Fc: 0.9479 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.468 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.494 / SU Rfree Blow DPI: 0.281 / SU Rfree Cruickshank DPI: 0.282
RfactorNum. reflection% reflectionSelection details
Rfree0.2433 1451 10 %RANDOM
Rwork0.187 ---
obs0.1927 14515 99.93 %-
Displacement parametersBiso max: 176.62 Å2 / Biso mean: 70.32 Å2 / Biso min: 19.21 Å2
Baniso -1Baniso -2Baniso -3
1-1.6448 Å20 Å20 Å2
2--1.6448 Å20 Å2
3----3.2895 Å2
Refine analyzeLuzzati coordinate error free: 0.385 Å
Refinement stepCycle: final / Resolution: 2.62→23.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2774 0 30 48 2852
Biso mean--62.13 40.88 -
Num. residues----343
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1003SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes82HARMONIC2
X-RAY DIFFRACTIONt_gen_planes405HARMONIC5
X-RAY DIFFRACTIONt_it2866HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion357SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3632SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2866HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3885HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion2.61
X-RAY DIFFRACTIONt_other_torsion20.33
LS refinement shellResolution: 2.62→2.83 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2739 294 10.06 %
Rwork0.2086 2628 -
all0.2149 2922 -
obs--99.93 %
Refinement TLS params.Method: refined / Details: FPPS / Origin x: 10.1454 Å / Origin y: 79.8974 Å / Origin z: 26.6041 Å
111213212223313233
T-0.3369 Å2-0.0222 Å20.0063 Å2--0.3439 Å20.0476 Å2--0.3978 Å2
L3.5057 °20.7786 °2-1.7105 °2-2.0897 °2-0.7591 °2--2.1245 °2
S-0.1355 Å °-0.1827 Å °-0.5451 Å °0.0245 Å °0.0196 Å °0.2071 Å °0.1924 Å °-0.0266 Å °0.1159 Å °
Refinement TLS groupSelection: all / Selection details: { F|* }

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