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- PDB-3n1v: Human FPPS COMPLEX WITH FBS_01 -

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Basic information

Entry
Database: PDB / ID: 3n1v
TitleHuman FPPS COMPLEX WITH FBS_01
ComponentsFARNESYL PYROPHOSPHATE SYNTHASEDimethylallyltranstransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / BISPHOSPHONATE / FRAGMENT-BASED SCREENING / TRANSFERASE / ISOPRENE BIOSYNTHESIS / CHOLESTEROL BIOSYNTHESIS / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / dimethylallyltranstransferase activity / Cholesterol biosynthesis / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / RNA binding ...geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / dimethylallyltranstransferase activity / Cholesterol biosynthesis / 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-3N1 / PHOSPHATE ION / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.18 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 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 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)40,7604
Polymers40,1841
Non-polymers5763
Water2,072115
1
F: FARNESYL PYROPHOSPHATE SYNTHASE
hetero molecules

F: FARNESYL PYROPHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5208
Polymers80,3682
Non-polymers1,1536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4590 Å2
ΔGint-37 kcal/mol
Surface area29270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.372, 111.372, 77.512
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein FARNESYL PYROPHOSPHATE SYNTHASE / Dimethylallyltranstransferase


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-3N1 / (5-chloro-3-methyl-1-benzothiophen-2-yl)acetic acid


Mass: 240.706 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H9ClO2S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.99 Å3/Da / Density % sol: 58.87 %
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: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97933 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 7, 2004
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.18→41.9 Å / Num. all: 26012 / Num. obs: 25863 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 40.6 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 24.03
Reflection shellResolution: 2.18→2.25 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 8.3 / Num. unique all: 2302 / % possible all: 99.9

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Processing

Software
NameClassification
XDSdata scaling
CNXrefinement
XDSdata reduction
XSCALEdata scaling
CNXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.18→41.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2654191.31 / 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
Rfree0.243 2160 8.4 %RANDOM
Rwork0.218 ---
all0.22 26012 --
obs0.22 25863 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.0121 Å2 / ksol: 0.383398 e/Å3
Displacement parametersBiso mean: 55.9 Å2
Baniso -1Baniso -2Baniso -3
1--11.72 Å20 Å20 Å2
2---11.72 Å20 Å2
3---23.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.18→41.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2774 0 35 115 2924
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it21.5
X-RAY DIFFRACTIONc_mcangle_it3.042
X-RAY DIFFRACTIONc_scbond_it2.912
X-RAY DIFFRACTIONc_scangle_it4.192.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.18→2.32 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.265 216 5.1 %
Rwork0.252 4031 -
obs-4031 99.9 %

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