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- PDB-4h5c: Crystal structure of human FPPS in ternary complex with YS0470 an... -

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Basic information

Entry
Database: PDB / ID: 4h5c
TitleCrystal structure of human FPPS in ternary complex with YS0470 and inorganic phosphate
ComponentsFarnesyl pyrophosphate synthaseDimethylallyltranstransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Transferase / 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
PHOSPHATE ION / Chem-YS4 / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.02 Å
AuthorsPark, J. / Lin, Y.-S. / Tsantrizos, Y.S. / Berghuis, A.M.
CitationJournal: Bmc Struct.Biol. / Year: 2012
Title: Ternary complex structures of human farnesyl pyrophosphate synthase bound with a novel inhibitor and secondary ligands provide insights into the molecular details of the enzyme's active site closure.
Authors: Park, J. / Lin, Y.S. / De Schutter, J.W. / Tsantrizos, Y.S. / Berghuis, A.M.
History
DepositionSep 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 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)43,7156
Polymers43,1451
Non-polymers5705
Water2,360131
1
F: Farnesyl pyrophosphate synthase
hetero molecules

F: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,43012
Polymers86,2902
Non-polymers1,14010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3970 Å2
ΔGint-27 kcal/mol
Surface area26350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.979, 110.979, 66.785
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 / 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-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 / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30% PEG 300, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 6, 2011
RadiationMonochromator: Confocal blue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. all: 28025 / Num. obs: 28025 / % possible obs: 99.9 % / Redundancy: 26.4 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 36.9
Reflection shellResolution: 2.02→2.05 Å / Redundancy: 24.1 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 5.7 / Num. unique all: 1369 / % possible all: 100

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Processing

Software
NameVersionClassification
StructureStudiodata collection
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.6.0117phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4DEM

4dem


Resolution: 2.02→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.585 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21317 1401 5 %RANDOM
Rwork0.18 ---
all0.1816 26374 --
obs0.1816 26374 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.231 Å2
Baniso -1Baniso -2Baniso -3
1--2.45 Å20 Å20 Å2
2---2.45 Å2-0 Å2
3---4.9 Å2
Refinement stepCycle: LAST / Resolution: 2.02→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2689 0 34 131 2854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022804
X-RAY DIFFRACTIONr_angle_refined_deg1.8431.9793824
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4385353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.30324.711121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.44515452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6971510
X-RAY DIFFRACTIONr_chiral_restr0.1260.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212124
LS refinement shellResolution: 2.02→2.067 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 83 -
Rwork0.2 1659 -
obs-1742 92.41 %
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)
13.3779-2.92924.03086.726-3.23229.6002-0.1169-0.3420.1701-0.02590.16350.3238-0.5396-0.7952-0.04660.19350.0520.06960.3716-0.01380.1985-1.049729.62898.0229
217.8045-8.75219.0874.3051-4.47094.64470.0121-0.9746-1.1398-0.00360.48440.52090.0147-0.4995-0.49650.644-0.02330.06160.73760.11940.676812.198116.823721.1158
34.53440.04832.55270.92190.34411.9739-0.1198-0.2760.33120.14150.04180.116-0.099-0.20640.0780.07730.02270.0450.1464-0.00060.09038.966127.86668.367
44.7491-1.04231.44682.2779-1.24130.89210.019-0.7438-0.02830.22160.13250.4219-0.062-0.2918-0.15160.211-0.03920.04480.3966-0.02290.2335-10.442220.27014.0045
53.00451.15420.29142.03250.03230.86090.0446-0.1878-0.0530.0987-0.00710.10580.0003-0.1409-0.03750.0390.0197-0.00190.04370.00820.013512.586524.18052.4311
62.61942.0522-1.82365.3095-3.33365.0528-0.05420.33410.0633-0.2749-0.025-0.2942-0.11270.24580.07910.0980.031-0.00450.15360.00160.050721.873228.1549-16.9544
72.50690.9207-0.4131.3285-0.34490.9394-0.04190.25830.2802-0.16220.09020.1167-0.0878-0.0101-0.04830.09080.0197-0.04050.12510.03380.075812.427935.7165-16.5209
820.504917.2042-1.922119.3989-4.94273.44750.14780.09690.46130.1847-0.367-0.1769-0.31220.23650.21920.14020.0359-0.04310.21080.05880.1543-1.626436.4062-21.4738
94.3257-0.2764-0.35244.29040.44365.19160.0343-0.01820.1730.0990.05270.0208-0.260.0679-0.0870.06750.0402-0.03460.1660.00660.1218-5.923630.3169-14.1273
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1F8 - 28
2X-RAY DIFFRACTION2F29 - 35
3X-RAY DIFFRACTION3F36 - 68
4X-RAY DIFFRACTION4F69 - 86
5X-RAY DIFFRACTION5F87 - 163
6X-RAY DIFFRACTION6F164 - 190
7X-RAY DIFFRACTION7F191 - 316
8X-RAY DIFFRACTION8F317 - 327
9X-RAY DIFFRACTION9F328 - 353

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