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- PDB-4nfj: Crystal structure of human FPPS in complex with magnesium, JDS051... -

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Basic information

Entry
Database: PDB / ID: 4nfj
TitleCrystal structure of human FPPS in complex with magnesium, JDS05120, and sulfate
ComponentsFarnesyl pyrophosphate synthaseDimethylallyltranstransferase
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 / 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 / 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
Chem-JD5 / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.05 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)43,7146
Polymers43,1451
Non-polymers5695
Water1,892105
1
F: Farnesyl pyrophosphate synthase
hetero molecules

F: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,42812
Polymers86,2902
Non-polymers1,13810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5080 Å2
ΔGint-114 kcal/mol
Surface area26500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.235, 111.235, 67.919
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 / 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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.43 Å3/Da / Density % sol: 49.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 25.5% PEG MME 2000, 0.17M ammonium sulfate, 15% glycerol, 0.09M sodium acetate, pH 4.6, 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: 2.05→50 Å / Num. all: 27177 / Num. obs: 27177 / % possible obs: 99.4 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 31.3
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 4 / Num. unique all: 1311 / % possible all: 98.6

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Processing

Software
NameVersionClassification
MxDCdata collection
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0049phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 4DEM

4dem


Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 10.68 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2125 1360 5 %RANDOM
Rwork0.1735 ---
all0.17549 25777 --
obs0.17549 25777 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.148 Å2
Baniso -1Baniso -2Baniso -3
1--2.7 Å20 Å20 Å2
2---2.7 Å20 Å2
3---5.39 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2709 0 34 105 2848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022800
X-RAY DIFFRACTIONr_bond_other_d0.0030.022608
X-RAY DIFFRACTIONr_angle_refined_deg1.8911.9783809
X-RAY DIFFRACTIONr_angle_other_deg0.953.0015976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3935342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.05724.809131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94915458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.771512
X-RAY DIFFRACTIONr_chiral_restr0.110.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023185
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02646
X-RAY DIFFRACTIONr_mcbond_it2.0782.8661371
X-RAY DIFFRACTIONr_mcbond_other2.0712.8641370
X-RAY DIFFRACTIONr_mcangle_it2.8054.2841712
X-RAY DIFFRACTIONr_mcangle_other2.8044.2861713
X-RAY DIFFRACTIONr_scbond_it3.0753.2421429
X-RAY DIFFRACTIONr_scbond_other3.0743.2411426
X-RAY DIFFRACTIONr_scangle_other4.6424.7392089
X-RAY DIFFRACTIONr_long_range_B_refined6.27424.5183408
X-RAY DIFFRACTIONr_long_range_B_other6.27424.3163372
LS refinement shellResolution: 2.051→2.104 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 116 -
Rwork0.272 1851 -
obs-1967 98.79 %
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)
16.1033-2.32843.88795.232-2.68610.4974-0.0106-0.6461-0.26120.22850.36840.5249-0.2385-0.8329-0.35790.15340.06130.07590.3488-0.07380.20370.554328.29399.4729
23.15310.17331.04712.06870.16281.72730.0109-0.38290.16750.12970.05470.1914-0.1358-0.3124-0.06560.04080.04130.02240.0964-0.00030.03859.484927.27044.7804
32.27910.9883-0.51322.8748-1.02941.5589-0.07560.16480.1895-0.26660.0910.0767-0.03890.0849-0.01540.07680.0182-0.04220.1174-0.01750.04713.254231.6441-14.3046
42.91210.901-1.07693.9621-1.69673.87650.07390.00940.3019-0.00080.0430.369-0.1185-0.0887-0.11690.08740.0145-0.09410.17790.03210.1807-4.729631.6251-17.5126
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1F8 - 33
2X-RAY DIFFRACTION2F34 - 140
3X-RAY DIFFRACTION3F141 - 315
4X-RAY DIFFRACTION4F316 - 350

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