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- PDB-4nfi: Crystal structure of human FPPS in complex with magnesium and JDS05120 -

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Basic information

Entry
Database: PDB / ID: 4nfi
TitleCrystal structure of human FPPS in complex with magnesium and JDS05120
ComponentsFarnesyl pyrophosphate synthase
KeywordsTransferase/Transferase inhibitor / 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
Chem-JD5 / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.85 Å
AuthorsPark, J. / De Schutter, J.W. / Tsantrizos, Y.S. / Berghuis, A.M.
CitationJournal: PLoS ONE / Year: 2017
Title: Crystallographic and thermodynamic characterization of phenylaminopyridine bisphosphonates binding to human farnesyl pyrophosphate synthase.
Authors: Park, J. / Rodionov, D. / De Schutter, J.W. / Lin, Y.S. / Tsantrizos, Y.S. / Berghuis, A.M.
History
DepositionOct 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 20, 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_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)43,6185
Polymers43,1451
Non-polymers4734
Water3,693205
1
F: Farnesyl pyrophosphate synthase
hetero molecules

F: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,23610
Polymers86,2902
Non-polymers9468
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4670 Å2
ΔGint-82 kcal/mol
Surface area26940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.510, 110.510, 66.970
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 / FPP synthase / FPS / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / ...FPP synthase / FPS / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl diphosphate synthase / Geranyltranstransferase


Mass: 43144.980 Da / Num. of mol.: 1
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-JD5 / [({5-[4-(cyclopropyloxy)phenyl]pyridin-3-yl}amino)methanediyl]bis(phosphonic acid)


Mass: 400.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H18N2O7P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.37 Å3/Da / Density % sol: 48.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 20% PEG 3350, 0.2M magnesium formate, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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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 20, 2013
RadiationMonochromator: ACCEL/BRUKER DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.85→50.85 Å / Num. all: 35614 / Num. obs: 35614 / % possible obs: 99.1 % / Redundancy: 9.6 % / Biso Wilson estimate: 24.99 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 29.54
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 4.98 / Num. unique all: 2598 / % possible all: 99.3

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Processing

Software
NameVersionClassification
MxDCdata collection
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0049phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 4DEM

4dem


Resolution: 1.85→50.85 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 6.216 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19639 1781 5 %RANDOM
Rwork0.16464 ---
all0.16622 33802 --
obs0.16622 33802 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.23 Å2
Baniso -1Baniso -2Baniso -3
1--2.53 Å20 Å20 Å2
2---2.53 Å20 Å2
3---5.06 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2748 0 29 205 2982
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022879
X-RAY DIFFRACTIONr_bond_other_d0.0030.022726
X-RAY DIFFRACTIONr_angle_refined_deg1.8571.9793913
X-RAY DIFFRACTIONr_angle_other_deg0.9843.0016260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2565352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42424.706136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.81815493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6131514
X-RAY DIFFRACTIONr_chiral_restr0.1320.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023281
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02668
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_it1.6752.0581399
X-RAY DIFFRACTIONr_mcbond_other1.6712.0571398
X-RAY DIFFRACTIONr_mcangle_it2.2663.0741754
X-RAY DIFFRACTIONr_mcangle_other2.2663.0751755
X-RAY DIFFRACTIONr_scbond_it2.5932.3741480
X-RAY DIFFRACTIONr_scbond_other2.5922.3751481
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8943.4482157
X-RAY DIFFRACTIONr_long_range_B_refined6.30518.2243627
X-RAY DIFFRACTIONr_long_range_B_other6.23617.7073540
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.851→1.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 121 -
Rwork0.261 2472 -
obs-2593 99.35 %
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)
17.7504-4.34314.51557.5637-3.51856.0106-0.1538-0.6007-0.00470.33130.31030.2703-0.4125-0.5284-0.15650.18530.04050.08720.3427-0.03340.15540.253328.19.6543
21.62230.54470.54791.3241-0.08131.45920.0081-0.37570.22070.16120.00980.3173-0.0577-0.3163-0.01790.06640.01460.02720.1244-0.01640.08459.098127.58784.5289
33.55651.4703-1.60783.4675-2.35574.43640.00740.0008-0.1921-0.19630.00880.04010.09880.1761-0.01620.04840.0221-0.03390.0285-0.01940.034513.053521.0186-8.6843
42.74790.57850.11991.5975-0.21610.902-0.05430.32340.3144-0.26520.08990.1808-0.10230.0336-0.03560.11190.006-0.03830.09020.03020.052812.034236.3852-17.0817
53.6545-0.0797-0.46863.73740.73535.30220.0466-0.09110.20670.12850.08030.0225-0.3185-0.0248-0.1270.09580.026-0.06980.1320.0260.1328-5.712530.3004-14.8709
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1F8 - 35
2X-RAY DIFFRACTION2F36 - 137
3X-RAY DIFFRACTION3F138 - 196
4X-RAY DIFFRACTION4F197 - 324
5X-RAY DIFFRACTION5F325 - 353

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