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- PDB-4pvy: Crystal structure of human FPPS in complex with [({5-[4-(propan-2... -

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Basic information

Entry
Database: PDB / ID: 4pvy
TitleCrystal structure of human FPPS in complex with [({5-[4-(propan-2-yloxy)phenyl]pyridin-3-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 / 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 / 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-JD1 / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.05 Å
AuthorsRodionov, D. / Park, 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
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)43,7126
Polymers43,1451
Non-polymers5675
Water4,342241
1
F: Farnesyl pyrophosphate synthase
hetero molecules

F: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,42512
Polymers86,2902
Non-polymers1,13510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5330 Å2
ΔGint-87 kcal/mol
Surface area26820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.060, 111.060, 67.030
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-658-

HOH

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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-JD1 / [({5-[4-(propan-2-yloxy)phenyl]pyridin-3-yl}amino)methanediyl]bis(phosphonic acid)


Mass: 402.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H20N2O7P2
#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.: 241 / 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: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.7M sodium chloride, 15% glycerol, 0.085M 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 10, 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: 2.05→111.06 Å / Num. all: 26578 / Num. obs: 26578 / % possible obs: 98.8 % / Redundancy: 32.9 % / Biso Wilson estimate: 22.614 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 44.1
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 3 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1769 / % possible all: 90.9

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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: 2.05→111.06 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.672 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20573 1288 4.9 %RANDOM
Rwork0.15999 ---
all0.1622 25246 --
obs0.1622 25246 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.252 Å2
Baniso -1Baniso -2Baniso -3
1--1.98 Å20 Å20 Å2
2---1.98 Å20 Å2
3---3.96 Å2
Refinement stepCycle: LAST / Resolution: 2.05→111.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2769 0 35 241 3045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022914
X-RAY DIFFRACTIONr_bond_other_d0.0010.022747
X-RAY DIFFRACTIONr_angle_refined_deg1.7861.9793964
X-RAY DIFFRACTIONr_angle_other_deg0.9193.0026315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.625361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88724.789142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88515501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7951515
X-RAY DIFFRACTIONr_chiral_restr0.1130.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023327
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02675
X-RAY DIFFRACTIONr_mcbond_it1.3161.5851405
X-RAY DIFFRACTIONr_mcbond_other1.3141.5841404
X-RAY DIFFRACTIONr_mcangle_it2.0132.3691761
X-RAY DIFFRACTIONr_mcangle_other2.0132.371762
X-RAY DIFFRACTIONr_scbond_it1.9431.8241509
X-RAY DIFFRACTIONr_scbond_other1.9431.8241509
X-RAY DIFFRACTIONr_scangle_other3.0292.6572198
X-RAY DIFFRACTIONr_long_range_B_refined6.58114.3883758
X-RAY DIFFRACTIONr_long_range_B_other6.5814.3963759
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 85 -
Rwork0.242 1683 -
obs-1768 89.93 %
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)
18.1652-2.27125.81917.3831-3.270410.0563-0.0358-0.66650.08130.08760.23080.555-0.4756-0.718-0.1950.21680.05380.09270.4097-0.06580.1328-0.995329.56218.5684
26.25970.40052.80970.02830.17681.2658-0.0382-0.35130.02280.003-0.0026-0.0172-0.0386-0.16810.04070.33320.0289-0.0050.31790.02770.318412.484916.250521.0765
35.68650.48763.61461.31560.35292.9095-0.019-0.43210.45660.0717-0.10010.2187-0.0423-0.32520.11920.09120.0280.0450.1956-0.02230.125.734726.79036.7895
42.92620.98780.54591.6891-0.02261.06030.1136-0.2923-0.05690.1186-0.070.1080.0385-0.1946-0.04360.0730.0235-0.010.07730.00240.016910.552923.4061.0059
54.49412.3729-0.99312.8545-1.10762.2054-0.1330.3052-0.1359-0.33440.073-0.03160.07460.03830.06010.11880.032-0.04810.0971-0.00620.04258.219324.8494-15.746
63.05120.43810.05472.50590.0112.5076-0.07220.33170.5134-0.24590.12410.0927-0.20130.1094-0.0520.154-0.0083-0.03410.11660.0690.098218.723144.0503-18.3808
73.60621.1171-0.74273.0128-1.84452.54890.07810.17550.18690.0852-0.02140.2116-0.1220.0019-0.05670.11840.0258-0.06660.18320.0370.0892-5.09931.1974-18.1353
83.61782.27334.21961.42992.67565.7966-0.0384-0.05350.3085-0.0259-0.02050.1806-0.36320.10010.0590.2784-0.00130.01510.1966-0.03170.2719-0.981138.9282-9.7055
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1F8 - 29
2X-RAY DIFFRACTION2F30 - 35
3X-RAY DIFFRACTION3F36 - 73
4X-RAY DIFFRACTION4F74 - 178
5X-RAY DIFFRACTION5F179 - 237
6X-RAY DIFFRACTION6F238 - 314
7X-RAY DIFFRACTION7F315 - 345
8X-RAY DIFFRACTION8F346 - 353

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