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- PDB-4lfv: Crystal structure of human FPPS in complex with YS0470 and two mo... -

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Basic information

Entry
Database: PDB / ID: 4lfv
TitleCrystal structure of human FPPS in complex with YS0470 and two molecules of inorganic phosphate
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 / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / Cholesterol biosynthesis / geranyltranstransferase activity / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / RNA binding ...geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / Cholesterol biosynthesis / 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 2. / Polyprenyl synthases signature 1. / 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 / Chem-YS4 / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsPark, J. / Lin, Y.-S. / Tsantrizos, Y.S. / Berghuis, A.M.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: Structure of human farnesyl pyrophosphate synthase in complex with an aminopyridine bisphosphonate and two molecules of inorganic phosphate.
Authors: Park, J. / Lin, Y.S. / Tsantrizos, Y.S. / Berghuis, A.M.
History
DepositionJun 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
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

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Assembly

Deposited unit
F: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8468
Polymers43,1451
Non-polymers7017
Water2,756153
1
F: Farnesyl pyrophosphate synthase
hetero molecules

F: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,69116
Polymers86,2902
Non-polymers1,40114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5920 Å2
ΔGint-138 kcal/mol
Surface area26080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.020, 111.020, 67.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11F-653-

HOH

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Components

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Protein , 1 types, 1 molecules F

#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 / Fragment: UNP residues 1-353
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

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Non-polymers , 5 types, 160 molecules

#2: Chemical ChemComp-YS4 / [({4-[4-(propan-2-yloxy)phenyl]pyridin-2-yl}amino)methanediyl]bis(phosphonic acid)


Mass: 402.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H20N2O7P2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% PEG400, 0.2 M magnesium chloride, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.15K

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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 25, 2012
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→67.04 Å / Num. all: 28844 / Num. obs: 28762 / % possible obs: 99.7 % / Redundancy: 14.3 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 28.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 7.4 / Num. unique all: 2083 / % possible all: 98.8

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Processing

Software
NameVersionClassification
MxDCdata collection
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.7.0032phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 4H5D

4h5d


Resolution: 2→51.03 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.802 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21791 1454 5.1 %RANDOM
Rwork0.17646 ---
all0.1786 27134 --
obs0.1786 27134 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.973 Å2
Baniso -1Baniso -2Baniso -3
1--2.94 Å20 Å20 Å2
2---2.94 Å20 Å2
3---5.87 Å2
Refinement stepCycle: LAST / Resolution: 2→51.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2728 0 40 153 2921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022879
X-RAY DIFFRACTIONr_bond_other_d0.0010.022695
X-RAY DIFFRACTIONr_angle_refined_deg1.9231.9813922
X-RAY DIFFRACTIONr_angle_other_deg0.8953.0026190
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.475353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48824.855138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58515482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7691513
X-RAY DIFFRACTIONr_chiral_restr0.120.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023293
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02665
X-RAY DIFFRACTIONr_mcbond_it3.093.2951397
X-RAY DIFFRACTIONr_mcbond_other3.0813.2941396
X-RAY DIFFRACTIONr_mcangle_it3.8364.9171755
X-RAY DIFFRACTIONr_mcangle_other3.8354.9181756
X-RAY DIFFRACTIONr_scbond_it3.9783.681482
X-RAY DIFFRACTIONr_scbond_other3.9713.6781475
X-RAY DIFFRACTIONr_scangle_other5.7455.372156
X-RAY DIFFRACTIONr_long_range_B_refined7.07527.1893622
X-RAY DIFFRACTIONr_long_range_B_other7.04927.0363557
LS refinement shellResolution: 2→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 110 -
Rwork0.202 1882 -
obs-1992 94.5 %

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