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- PDB-3n6k: Human FPPS complex with NOV_823 -

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Basic information

Entry
Database: PDB / ID: 3n6k
TitleHuman FPPS complex with NOV_823
ComponentsFARNESYL PYROPHOSPHATE SYNTHASE
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / BISPHOSPHONATE / FRAGMENT-BASED SCREENING / TRANSFERASE / ISOPRENE BIOSYNTHESIS / CHOLESTEROL BIOSYNTHESIS / RANSFERASE-TRANSFERASE INHIBITOR complex / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / Cholesterol biosynthesis / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / peroxisome ...geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / Cholesterol biosynthesis / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / peroxisome / mitochondrial matrix / 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-BFH / PHOSPHATE ION / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.25 Å
AuthorsRondeau, J.-M.
Citation
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.
#1: Journal: ChemMedChem / Year: 2006
Title: Structural basis for the exceptional in vivo efficacy of bisphosphonate drugs
Authors: Rondeau, J.M. / Bitsch, F. / Bourgier, E. / Geiser, M. / Hemmig, R. / Kroemer, M. / Lehmann, S. / Ramage, P. / Rieffel, S. / Strauss, A. / Green, J.R. / Jahnke, W.
History
DepositionMay 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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
F: FARNESYL PYROPHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5483
Polymers40,1841
Non-polymers3642
Water2,054114
1
F: FARNESYL PYROPHOSPHATE SYNTHASE
hetero molecules

F: FARNESYL PYROPHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0966
Polymers80,3682
Non-polymers7284
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4490 Å2
ΔGint-39 kcal/mol
Surface area28950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.123, 111.123, 76.779
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 / FPP synthase / FPS / Farnesyl diphosphate synthase / Dimethylallyltranstransferase / Geranyltranstransferase


Mass: 40183.855 Da / Num. of mol.: 1 / Fragment: 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 (E. coli) / Strain (production host): BL21 TUNER (DE3)
References: UniProt: P14324, dimethylallyltranstransferase, (2E,6E)-farnesyl diphosphate synthase
#2: Chemical ChemComp-BFH / 1-(carboxymethyl)-1H-benzo[g]indole-2-carboxylic acid


Mass: 269.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H11NO4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.95 Å3/Da / Density % sol: 58.29 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 1.2M sodium potassium phosphate, 25% glycerol, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: SATURN92 / Detector: CCD / Date: Mar 15, 2005 / Details: Mirrors
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 22485 / Num. obs: 22485 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.9 % / Biso Wilson estimate: 45.3 Å2 / Rmerge(I) obs: 0.1 / Χ2: 1.058 / Net I/σ(I): 8.4
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.455 / Num. unique all: 2295 / Χ2: 0.707 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNXphasing
CNXrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.25→26.12 Å / Rfactor Rfree error: 0.011 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 18665152 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.338 999 4.8 %RANDOM
Rwork0.262 ---
all0.265 20605 --
obs0.265 20605 88.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.016 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso max: 115.84 Å2 / Biso mean: 61.774 Å2 / Biso min: 26.48 Å2
Baniso -1Baniso -2Baniso -3
1--14.52 Å20 Å20 Å2
2---14.52 Å20 Å2
3---29.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.25→26.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2759 0 25 114 2898
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.592
X-RAY DIFFRACTIONc_scbond_it2.832
X-RAY DIFFRACTIONc_scangle_it3.772.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.391 170 4.7 %
Rwork0.355 3480 -
all-3650 -
obs-3650 95.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4NOV_823.PARAMNOV_823.TOP

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