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- PDB-4xqr: Crystal structure of unliganded human FPPS at 2.15 angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 4xqr
TitleCrystal structure of unliganded human FPPS at 2.15 angstrom resolution
ComponentsFarnesyl pyrophosphate synthase
KeywordsTRANSFERASE
Function / homology
Function and homology information


geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / Cholesterol biosynthesis / trans, trans-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 / trans, trans-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
PHOSPHATE ION / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 Å
AuthorsPark, J. / Berghuis, A.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Fonds de recherche Nature et technologies Canada
CitationJournal: J.Struct.Biol. / Year: 2026
Title: Discovery and computational characterization of a novel cryptic pocket in human farnesyl pyrophosphate synthase.
Authors: Pandya, V. / Wilson, K.A. / Leung, C.Y. / Tsantrizos, Y.S. / Park, J.
History
DepositionJan 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 8, 2026Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)43,2402
Polymers43,1451
Non-polymers951
Water1,04558
1
F: Farnesyl pyrophosphate synthase
hetero molecules

F: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4804
Polymers86,2902
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4360 Å2
ΔGint-43 kcal/mol
Surface area27750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.850, 110.850, 78.080
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 / 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


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


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.78 Å3/Da / Density % sol: 55.75 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 17% PEG 4000, 8.5% 2-propanol, 15% glycerol, 0.09 M HEPES

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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: Feb 13, 2013
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: 2.15→55.42 Å / Num. obs: 26862 / % possible obs: 99.7 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 13.9
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.991 / Mean I/σ(I) obs: 2.5 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0073phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2F7M

2f7m


Resolution: 2.15→55.42 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 13.9 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22475 1370 5.1 %RANDOM
Rwork0.18502 ---
obs0.18703 25437 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.975 Å2
Baniso -1Baniso -2Baniso -3
1--4.34 Å20 Å20 Å2
2---4.34 Å20 Å2
3---8.67 Å2
Refinement stepCycle: 1 / Resolution: 2.15→55.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2664 0 5 58 2727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192727
X-RAY DIFFRACTIONr_bond_other_d0.0010.022548
X-RAY DIFFRACTIONr_angle_refined_deg1.751.9653710
X-RAY DIFFRACTIONr_angle_other_deg0.88435827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2945340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52524.516124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.01515437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.31512
X-RAY DIFFRACTIONr_chiral_restr0.0930.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023116
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02632
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_it2.8713.9451363
X-RAY DIFFRACTIONr_mcbond_other2.873.9441362
X-RAY DIFFRACTIONr_mcangle_it4.3585.9081702
X-RAY DIFFRACTIONr_mcangle_other4.3575.9091703
X-RAY DIFFRACTIONr_scbond_it3.5574.1691364
X-RAY DIFFRACTIONr_scbond_other3.5584.1571361
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2196.1232003
X-RAY DIFFRACTIONr_long_range_B_refined7.11232.0653296
X-RAY DIFFRACTIONr_long_range_B_other7.04831.9333279
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.153→2.209 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 97 -
Rwork0.314 1807 -
obs--98.86 %
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)
14.4988-0.1421-1.4253.028-0.28872.2576-0.05670.3999-0.2719-0.43570.08790.49740.2315-0.5274-0.03120.1423-0.0669-0.06390.16720.00280.09929.541184.599816.3939
25.6278-0.7970.3473.6291-1.89633.5137-0.0025-0.5019-0.81360.3326-0.1257-0.00350.41320.47840.12820.25140.01730.05060.36670.05050.143810.785976.184539.361
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1F9 - 176
2X-RAY DIFFRACTION2F177 - 349

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