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- PDB-5dgm: Crystal structure of human FPPS in complex with monophosphonate c... -

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Basic information

Entry
Database: PDB / ID: 5dgm
TitleCrystal structure of human FPPS in complex with monophosphonate compound 7
ComponentsFarnesyl pyrophosphate synthase
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 / 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
Chem-59Z / PHOSPHATE ION / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.86 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. / Goette, 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. / Goette, 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 20, 2016Group: Database references
Revision 1.2May 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)40,6413
Polymers40,1841
Non-polymers4572
Water59433
1
F: Farnesyl pyrophosphate synthase
hetero molecules

F: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2826
Polymers80,3682
Non-polymers9144
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4630 Å2
ΔGint-40 kcal/mol
Surface area29160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.723, 110.723, 76.775
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 / 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: 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-59Z / {2-[(phosphonomethyl)carbamoyl]-1H-benzo[g]indol-1-yl}acetic acid


Mass: 362.274 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15N2O6P
#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.: 33 / 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: 2.93 Å3/Da / Density % sol: 57.99 %
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: Jun 12, 2006
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.86→78 Å / Num. obs: 11498 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Biso Wilson estimate: 65.24 Å2 / Rmerge F obs: 0.078 / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.1 / Net I/σ(I): 21.05 / Num. measured all: 157936
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.86-2.960.2610.4436.2914983109710950.4699.8
2.96-3.080.2310.4096.915749114611460.425100
3.08-3.210.1710.3038.8314501104910480.31599.9
3.21-3.360.1380.23910.9114273102410240.248100
3.36-3.530.1160.18113.66131729479470.188100
3.53-3.730.0740.13418.38129649259250.139100
3.73-3.970.0640.10321.97122878818810.107100
3.97-4.260.0520.0825.64115298288270.08399.9
4.26-4.630.0390.06431.38106147667650.06699.9
4.63-5.120.0330.05436.5399357167160.056100
5.12-5.790.0350.05834.0686216266250.0699.8
5.79-6.820.0350.05633.9375665595590.059100
6.82-8.720.020.0445.9662094744730.04199.8
8.72-13.910.0120.03354.4842463423400.03499.4
13.910.0160.04345.2412871301250.04696.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSDecember 2004data reduction
XSCALEDecember 2003data scaling
CNSCNX 2005phasing
Coot0.6.2model building
BUSTER-TNT1.11.2refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.86→54.8 Å / Cor.coef. Fo:Fc: 0.9358 / Cor.coef. Fo:Fc free: 0.9049 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.32 / SU Rfree Cruickshank DPI: 0.321
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 1145 9.96 %RANDOM
Rwork0.1846 ---
obs0.1889 11497 99.92 %-
Displacement parametersBiso max: 202.16 Å2 / Biso min: 21.51 Å2
Baniso -1Baniso -2Baniso -3
1-7.4486 Å20 Å20 Å2
2--7.4486 Å20 Å2
3----14.8973 Å2
Refine analyzeLuzzati coordinate error free: 0.399 Å
Refinement stepCycle: final / Resolution: 2.86→54.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2774 0 30 33 2837
Biso mean--81.72 44.3 -
Num. residues----343
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1018SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes82HARMONIC2
X-RAY DIFFRACTIONt_gen_planes404HARMONIC5
X-RAY DIFFRACTIONt_it2864HARMONIC20
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_contact3598SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2864HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3883HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion2.5
X-RAY DIFFRACTIONt_other_torsion20.66
LS refinement shellResolution: 2.86→3.13 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2857 248 9.22 %
Rwork0.191 2442 -
all0.1994 2690 -
obs--99.92 %
Refinement TLS params.Method: refined / Details: FPPS / Origin x: 10.3024 Å / Origin y: 79.7587 Å / Origin z: 27.4896 Å
111213212223313233
T-0.3316 Å2-0.0277 Å20.031 Å2--0.2553 Å20.0095 Å2--0.1338 Å2
L3.0486 °20.8834 °2-2.0112 °2-2.4886 °2-0.7812 °2--2.682 °2
S-0.2174 Å °-0.1408 Å °-0.3227 Å °0.0583 Å °0.0221 Å °0.3044 Å °0.1924 Å °-0.0229 Å °0.1953 Å °
Refinement TLS groupSelection: all / Selection details: { F|* }

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