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- PDB-3n1w: Human FPPS COMPLEX WITH FBS_02 -

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Basic information

Entry
Database: PDB / ID: 3n1w
TitleHuman FPPS COMPLEX WITH FBS_02
ComponentsFARNESYL PYROPHOSPHATE SYNTHASE
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 / (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 / cytoplasm / cytosol
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
(5-chloro-1-benzothiophen-3-yl)acetic acid / PHOSPHATE ION / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.56 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

Downloads & links

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Assembly

Deposited unit
F: FARNESYL PYROPHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5063
Polymers40,1841
Non-polymers3222
Water1,00956
1
F: FARNESYL PYROPHOSPHATE SYNTHASE
hetero molecules

F: FARNESYL PYROPHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0116
Polymers80,3682
Non-polymers6434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4560 Å2
ΔGint-38 kcal/mol
Surface area29190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.332, 111.332, 76.248
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


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-3N2 / (5-chloro-1-benzothiophen-3-yl)acetic acid


Mass: 226.679 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H7ClO2S
#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.: 56 / 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: 2.94 Å3/Da / Density % sol: 58.16 %
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: MARCCD165 / 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: 2.56→40 Å / Num. obs: 15908 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 54.408 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 18.97
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.56-2.640.3370.3486.110008137513740.3899.9
2.64-2.720.310.316.78826121512120.3399.8
2.72-2.810.2630.2687.48883122312210.2999.8
2.81-2.920.1970.2029.29355128612830.2299.8
2.92-3.030.1750.17310.47979110211010.1999.9
3.03-3.160.1350.145128164112811270.1699.9
3.16-3.30.10.10615.27423103010290.1199.9
3.3-3.470.0760.08617.57468103710360.0999.9
3.47-3.670.0580.06821.569789769750.0799.9
3.67-3.90.0420.05525.764319019010.06100
3.9-4.190.0330.04629.162238808790.0599.9
4.19-4.550.030.04331.655748008000.05100
4.55-5.020.0240.03934.751687527520.04100
5.02-5.670.0270.04233.944966636630.05100
5.67-6.670.0240.04133.639205915910.04100
6.67-8.480.0180.02842.131375015000.0399.8
8.48-13.30.0140.02647.718863653430.0394
13.30.0140.02140.44921471200.0281.6

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
APRVphasing
CNXrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.56→39.36 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.763 / Data cutoff high absF: 2787454 / 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
Rfree0.257 1603 10.1 %RANDOM
Rwork0.208 ---
all0.213 15908 --
obs0.213 15908 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.342 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso max: 128.87 Å2 / Biso mean: 65.566 Å2 / Biso min: 21.53 Å2
Baniso -1Baniso -2Baniso -3
1--20.27 Å20 Å20 Å2
2---20.27 Å20 Å2
3---40.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.56→39.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2774 0 19 56 2849
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_d18.5
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it3.271.5
X-RAY DIFFRACTIONc_mcangle_it5.042
X-RAY DIFFRACTIONc_scbond_it4.82
X-RAY DIFFRACTIONc_scangle_it6.752.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 32

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.56-2.590.377430.388450493
2.59-2.620.444600.373420480
2.62-2.650.392530.386442495
2.65-2.680.44450.363427472
2.68-2.710.382580.337447505
2.71-2.740.441440.324430474
2.74-2.780.404480.302438486
2.78-2.820.306550.317449504
2.82-2.860.408480.276426474
2.86-2.90.317440.285440484
2.9-2.950.279490.262449498
2.95-2.990.317390.262447486
2.99-3.050.336390.241453492
3.05-3.10.299540.269439493
3.1-3.160.412520.259440492
3.16-3.230.347490.246439488
3.23-3.30.271400.227459499
3.3-3.370.325600.221439499
3.37-3.460.282490.228437486
3.46-3.550.257500.215438488
3.55-3.650.263480.214457505
3.65-3.770.31430.212445488
3.77-3.910.241510.17449500
3.91-4.060.21660.156442508
4.06-4.250.23560.175444500
4.25-4.470.138510.126459510
4.47-4.750.193450.139456501
4.75-5.120.245550.155463518
5.12-5.630.225530.163459512
5.63-6.450.239380.21476514
6.45-8.120.283530.185480533
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3FBS_02.PRMION.TOP
X-RAY DIFFRACTION4ION.PARAM

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