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- PDB-5ja0: Crystal structure of human FPPS with allosterically bound FPP -

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Basic information

Entry
Database: PDB / ID: 5ja0
TitleCrystal structure of human FPPS with allosterically bound FPP
ComponentsFarnesyl pyrophosphate synthaseDimethylallyltranstransferase
KeywordsTRANSFERASE
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
FARNESYL DIPHOSPHATE / PHOSPHATE ION / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsPark, J. / Zielinski, M. / Tsantrizos, Y.S. / Berghuis, A.M.
CitationJournal: Nat Commun / Year: 2017
Title: Human farnesyl pyrophosphate synthase is allosterically inhibited by its own product.
Authors: Park, J. / Zielinski, M. / Magder, A. / Tsantrizos, Y.S. / Berghuis, A.M.
History
DepositionApr 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)43,6223
Polymers43,1451
Non-polymers4772
Water3,279182
1
F: Farnesyl pyrophosphate synthase
hetero molecules

F: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2456
Polymers86,2902
Non-polymers9554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area6330 Å2
ΔGint-50 kcal/mol
Surface area27100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.890, 110.890, 77.480
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 / FPS / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl ...FPS / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl diphosphate synthase / Geranyltranstransferase


Mass: 43144.980 Da / Num. of mol.: 1 / Fragment: UNP residues 67-419
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FDPS, FPS, KIAA1293 / Production host: Escherichia coli (E. coli)
References: UniProt: P14324, (2E,6E)-farnesyl diphosphate synthase, dimethylallyltranstransferase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-FPP / FARNESYL DIPHOSPHATE / Farnesyl pyrophosphate


Mass: 382.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O7P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.08 M TrisHCl, 1.6 M ammonium phosphate, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 19, 2014
RadiationMonochromator: ACCEL/Bruker double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.9→49.59 Å / Num. obs: 38509 / % possible obs: 99.8 % / Redundancy: 9.7 % / Biso Wilson estimate: 36.118 Å2 / CC1/2: 0.1 / Rmerge(I) obs: 0.039 / Net I/σ(I): 31.5
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 9.7 % / Rmerge(I) obs: 1.111 / Mean I/σ(I) obs: 2.4 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0123phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2F7M

2f7m


Resolution: 1.9→49.59 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 7.131 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2108 2025 5.3 %RANDOM
Rwork0.17201 ---
obs0.17401 36427 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.974 Å2
Baniso -1Baniso -2Baniso -3
1--2.62 Å20 Å20 Å2
2---2.62 Å20 Å2
3---5.24 Å2
Refinement stepCycle: LAST / Resolution: 1.9→49.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2595 0 29 182 2806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.022678
X-RAY DIFFRACTIONr_bond_other_d0.0020.022523
X-RAY DIFFRACTIONr_angle_refined_deg2.4031.9763636
X-RAY DIFFRACTIONr_angle_other_deg1.24635767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.585327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87524.298121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51515432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3891513
X-RAY DIFFRACTIONr_chiral_restr0.1590.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023030
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02623
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1522.91318
X-RAY DIFFRACTIONr_mcbond_other2.1512.9011319
X-RAY DIFFRACTIONr_mcangle_it2.9424.3281643
X-RAY DIFFRACTIONr_mcangle_other2.9434.3271643
X-RAY DIFFRACTIONr_scbond_it3.2033.211360
X-RAY DIFFRACTIONr_scbond_other3.2023.2111361
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7234.7121994
X-RAY DIFFRACTIONr_long_range_B_refined7.59125.0563328
X-RAY DIFFRACTIONr_long_range_B_other7.59125.0633329
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 150 -
Rwork0.308 2625 -
obs--99.04 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
111.85285.6282-7.90618.192-3.92418.47720.02070.58510.006-0.17270.1690.56690.2644-0.7778-0.18970.1698-0.1049-0.12720.2955-0.0480.19731.919680.436710.5324
26.52020.4142-4.86012.49120.35615.58460.02860.623-0.0226-0.36380.05270.43680.0392-0.6856-0.08130.0766-0.0416-0.07390.1502-0.00190.1185.57882.961314.2055
36.4355-2.5005-0.66073.8872-0.36351.7819-0.08740.2352-0.3218-0.20820.02670.26430.2182-0.27070.06070.0473-0.0418-0.00030.0488-0.01490.02513.214182.781215.9429
410.5019-5.48135.22856.4555-4.68476.47040.0084-0.30830.08870.08230.07510.2001-0.1939-0.0983-0.08360.0295-0.02620.02730.0397-0.03480.041912.04492.630325.7218
54.3519-0.80390.98853.924-1.99643.9679-0.0052-0.405-0.49910.4475-0.2084-0.20040.27620.53930.21360.16710.00180.04130.27980.0480.16213.683678.308338.4699
64.4-1.92552.15364.5679-2.76643.06760.0474-0.3093-0.59390.3328-0.09570.14780.39520.13050.04830.30910.01670.14460.2560.05640.31873.660173.913841.264
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1F10 - 30
2X-RAY DIFFRACTION2F36 - 76
3X-RAY DIFFRACTION3F77 - 147
4X-RAY DIFFRACTION4F148 - 178
5X-RAY DIFFRACTION5F179 - 293
6X-RAY DIFFRACTION6F294 - 350

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