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- PDB-4pvx: Crystal structure of human FPPS in complex with [({4-[4-(cyclopro... -

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Basic information

Entry
Database: PDB / ID: 4pvx
TitleCrystal structure of human FPPS in complex with [({4-[4-(cyclopropyloxy)phenyl]pyridin-2-yl}amino)methanediyl]bis(phosphonic acid)
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
Chem-YS1 / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.18 Å
AuthorsRodionov, D. / Park, J. / Lin, Y.-S. / 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
DepositionMar 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: 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 / _citation_author.name
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)43,7106
Polymers43,1451
Non-polymers5655
Water2,666148
1
F: Farnesyl pyrophosphate synthase
hetero molecules

F: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,42012
Polymers86,2902
Non-polymers1,13110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5440 Å2
ΔGint-82 kcal/mol
Surface area26820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.260, 111.260, 69.340
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-YS1 / [({4-[4-(cyclopropyloxy)phenyl]pyridin-2-yl}amino)methanediyl]bis(phosphonic acid)


Mass: 400.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H18N2O7P2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.49 Å3/Da / Density % sol: 50.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 5.6% PEG 4000, 30% glycerol, 0.07M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 7, 2014 / Details: Rigaku Varimax-HF
RadiationMonochromator: Rigaku Varimax-HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.18→69.34 Å / Num. all: 22981 / Num. obs: 22981 / % possible obs: 98.6 % / Redundancy: 19.7 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 53.8
Reflection shellResolution: 2.18→2.24 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1671 / % possible all: 98.9

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Processing

Software
NameVersionClassification
StructureStudiodata collection
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0049phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 4H5C

4h5c


Resolution: 2.18→69.34 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.93 / SU B: 10.451 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22008 1167 5.1 %RANDOM
Rwork0.16974 ---
all0.17229 21774 --
obs0.17229 21774 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.974 Å2
Baniso -1Baniso -2Baniso -3
1--2.82 Å20 Å20 Å2
2---2.82 Å20 Å2
3---5.63 Å2
Refinement stepCycle: LAST / Resolution: 2.18→69.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2751 0 35 148 2934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022859
X-RAY DIFFRACTIONr_bond_other_d0.0030.022699
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.9813883
X-RAY DIFFRACTIONr_angle_other_deg0.9093.0016201
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6215346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28924.82139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10115487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.671514
X-RAY DIFFRACTIONr_chiral_restr0.0950.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023242
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02659
X-RAY DIFFRACTIONr_mcbond_it1.6122.331378
X-RAY DIFFRACTIONr_mcbond_other1.612.3281377
X-RAY DIFFRACTIONr_mcangle_it2.3213.4841723
X-RAY DIFFRACTIONr_mcangle_other2.323.4861724
X-RAY DIFFRACTIONr_scbond_it2.2872.6311481
X-RAY DIFFRACTIONr_scbond_other2.2862.6311481
X-RAY DIFFRACTIONr_scangle_other3.5153.8372157
X-RAY DIFFRACTIONr_long_range_B_refined5.43819.9363541
X-RAY DIFFRACTIONr_long_range_B_other5.43819.9423542
LS refinement shellResolution: 2.18→2.237 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 84 -
Rwork0.25 1586 -
obs-1670 98.88 %
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)
19.3435-3.39368.43824.7181-3.927312.1301-0.159-0.74960.278-0.0010.30020.5392-0.4937-0.9797-0.14120.20520.10460.03850.3811-0.09530.2593-1.036829.79097.9215
24.5813-1.75832.6740.6844-1.04071.5835-0.0534-0.3995-0.38490.00380.21210.1149-0.0064-0.3113-0.15880.41730.0248-0.01530.5267-0.03860.407310.971117.352720.3759
34.89450.21543.11170.53570.3252.76610.0365-0.42370.29940.0702-0.10160.24310.0243-0.37030.06510.06770.04730.04890.1845-0.02010.18043.02525.79386.0481
43.41651.47420.29341.7855-0.33931.01790.0853-0.36930.11320.22-0.04090.1277-0.076-0.1611-0.04440.03920.02330.00860.0813-0.01340.016212.855627.093.9777
57.6474.7816-3.86035.1333-3.72724.23510.0706-0.0506-0.0787-0.09690.01880.17790.0935-0.0314-0.08930.04760.0269-0.03910.0291-0.01480.040411.813718.184-6.6237
64.972.788-1.18933.0748-1.35732.0458-0.10330.3162-0.2098-0.42130.07630.06210.0953-0.03450.02690.09880.0252-0.04440.0787-0.01170.04267.7424.5115-15.8471
73.45080.1432-0.01962.5432-0.02672.39120.00820.35410.5187-0.25550.0310.0294-0.30730.1099-0.03920.1334-0.0023-0.02420.09560.06920.101718.673644.0996-18.6478
84.72111.4476-1.58743.3444-2.82613.64010.07520.03530.38430.08860.01950.3083-0.21750.0273-0.09470.07270.0248-0.05580.16980.02630.1203-4.584731.7937-17.373
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1F8 - 28
2X-RAY DIFFRACTION2F29 - 35
3X-RAY DIFFRACTION3F36 - 78
4X-RAY DIFFRACTION4F79 - 147
5X-RAY DIFFRACTION5F148 - 181
6X-RAY DIFFRACTION6F182 - 236
7X-RAY DIFFRACTION7F237 - 315
8X-RAY DIFFRACTION8F316 - 350

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