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- PDB-4p0x: Human farnesyl diphosphate synthase in complex with Taxodione -

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Basic information

Entry
Database: PDB / ID: 4p0x
TitleHuman farnesyl diphosphate synthase in complex with Taxodione
ComponentsFarnesyl pyrophosphate synthaseDimethylallyltranstransferase
Keywordstransferase/transferase inhibitor / FPPS / Inhibitor / Complex / transferase-transferase inhibitor complex
Function / homology
Function and homology information


geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / dimethylallyltranstransferase activity / Cholesterol biosynthesis / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / RNA binding ...geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / dimethylallyltranstransferase activity / Cholesterol biosynthesis / 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-1WO / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLiu, Y.L. / Oldfield, E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA158191 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM065307 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Taxodione and arenarone inhibit farnesyl diphosphate synthase by binding to the isopentenyl diphosphate site.
Authors: Liu, Y.L. / Lindert, S. / Zhu, W. / Wang, K. / McCammon, J.A. / Oldfield, E.
History
DepositionFeb 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 2.0Sep 6, 2017Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: atom_site_anisotrop / citation ...atom_site_anisotrop / citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_ref
Item: _atom_site_anisotrop.pdbx_PDB_model_num / _atom_site_anisotrop.pdbx_label_asym_id ..._atom_site_anisotrop.pdbx_PDB_model_num / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_ref.biol_id
Revision 2.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6593
Polymers40,0301
Non-polymers6292
Water1,09961
1
A: Farnesyl pyrophosphate synthase
hetero molecules

A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3176
Polymers80,0592
Non-polymers1,2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area4030 Å2
ΔGint-23 kcal/mol
Surface area28370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.623, 110.623, 78.443
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Farnesyl pyrophosphate synthase / Dimethylallyltranstransferase / FPS / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl ...FPS / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl diphosphate synthase / Geranyltranstransferase


Mass: 40029.691 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-1WO / (5beta)-11-hydroxyabieta-7,9(11),13-triene-6,12-dione / taxodione


Mass: 314.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H26O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 3 Å3/Da / Density % sol: 58.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.2M sodium potassium phosphate, 25% glycerol, 1mM GPP
PH range: 5.0-5.4

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.3→55.31 Å / Num. obs: 22231 / % possible obs: 99.8 % / Redundancy: 11 % / Net I/σ(I): 44.04

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→55.31 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.884 / SU B: 19.155 / SU ML: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.378 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2791 880 5.1 %RANDOM
Rwork0.2074 16446 --
obs0.2109 17326 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.87 Å2 / Biso mean: 19.467 Å2 / Biso min: 5.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.11 Å20 Å2
3----0.21 Å2
Refinement stepCycle: final / Resolution: 2.5→55.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2657 0 46 61 2764
Biso mean--67.46 42.9 -
Num. residues----330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022760
X-RAY DIFFRACTIONr_bond_other_d0.0030.022640
X-RAY DIFFRACTIONr_angle_refined_deg1.761.9863747
X-RAY DIFFRACTIONr_angle_other_deg0.9653.0066061
X-RAY DIFFRACTIONr_chiral_restr0.0960.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023083
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02625
X-RAY DIFFRACTIONr_mcbond_it0.9571.7691315
X-RAY DIFFRACTIONr_mcbond_other0.9561.7681314
X-RAY DIFFRACTIONr_mcangle_it1.4792.651635
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 68 -
Rwork0.264 1192 -
all-1260 -
obs--100 %
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)
128.557510.771811.29057.20641.282323.0476-0.20150.43450.5233-1.1069-0.0851-1.0506-0.77362.87080.28670.5825-0.20670.43560.55770.00560.70682.748534.863-23.9758
227.892218.95056.377835.19120.866611.9039-0.32621.0583-0.542-1.28010.1702-0.6427-0.4661.10190.1560.2479-0.03980.10380.36130.06060.1073-6.067127.2188-32.8539
320.8218.7824-19.825716.9711-17.91318.9364-0.69620.9250.3323-0.77940.86680.21510.9175-0.7694-0.17071.27140.43180.24590.8654-0.23321.5355-16.458819.0727-41.6163
41.18343.58052.63214.681110.907414.3921-0.50780.49280.3475-1.24360.52340.2576-0.72791.5389-0.01560.2334-0.2365-0.19960.66160.31020.273-15.611131.6638-31.0739
517.865-6.17927.312812.7187-6.94816.66390.60750.8406-0.0336-0.7321-0.7014-1.04440.02051.09530.0940.1708-0.08890.09640.2985-0.03280.2823.945827.3694-16.1919
650.4965-9.3738-22.164614.13656.483910.19320.285-0.81561.2101-0.43990.4173-1.4194-0.18220.4636-0.70230.209-0.06440.05860.76350.16550.48436.377222.119-25.2692
713.6609-2.4596-1.27052.25190.30260.3669-0.1652-0.60880.74970.1450.1763-0.1611-0.15720.2114-0.01110.1529-0.0849-0.04550.13510.00880.0595-14.754129.5257-18.3791
85.1557-0.05073.978717.52018.6817.6527-0.26040.27220.7097-0.73640.3973-1.0364-1.01110.6496-0.13680.2274-0.0364-0.04960.04360.03210.2267-21.92939.3083-22.9651
96.9319-2.54242.69245.29630.48562.50540.2120.7492-0.6127-0.3662-0.0376-0.25350.17190.4905-0.17430.07740.00740.05370.143-0.05990.1595-10.345218.1416-23.3966
1019.9709-8.1968-13.44098.659810.039413.60790.1705-0.82740.2410.3112-0.26150.03540.2353-0.21640.09110.0568-0.0731-0.01040.218-0.05450.0647-19.596923.8192-7.9625
117.6592-6.03151.42255.8713-1.13610.26450.15210.06170.1985-0.6737-0.17560.92240.04160.00880.02350.8478-0.0879-0.31050.819-0.14751.1275-29.271934.44072.9774
129.3091-2.2687-2.34.56692.31283.0533-0.0834-0.4557-0.39540.70140.0364-0.08650.38060.04090.0470.1489-0.0506-0.07140.20770.03730.1078-7.824623.0887-5.0391
137.2831-10.43880.521925.74122.18592.267-0.0168-0.24070.50520.06770.0804-0.1877-0.1389-0.2972-0.06350.1612-0.0206-0.040.27830.00870.1358-7.583234.7582-1.2529
1428.87849.196718.63979.061313.101620.41030.21640.0288-0.71550.70890.1399-0.09930.93870.1938-0.35620.88030.09420.04710.65680.08220.862-9.396949.3693-10.1191
1511.4071-8.79494.16036.8689-3.61369.44890.08450.57780.324-0.1024-0.5488-0.0311-0.956-0.20870.46430.36070.0795-0.33670.4831-0.38380.9456-20.756142.0196-2.723
1625.7229-6.4079-20.188816.49070.203817.452-0.6048-0.18930.29641.98190.86710.5645-0.0902-0.3449-0.26230.44160.04820.08641.3079-0.83710.6516-22.28341.582411.8062
1711.53376.4206-2.429810.01593.023114.67220.1215-0.5941.17350.50370.36172.2831-0.4281-1.0346-0.48320.48090.22450.03860.9793-0.27671.2556-29.871445.9573.6258
184.449-0.83910.6142.02064.328910.72290.14591.2416-1.2278-0.79980.01010.2685-1.96020.6245-0.1560.97420.55020.11380.9531-0.19691.336-26.669552.48520.1983
1919.168-14.0716-0.329414.41081.06382.2352-0.0449-0.62890.85530.44910.00530.0408-0.3315-0.17980.03950.33980.0113-0.05920.3484-0.14490.3256-7.74541.73117.5743
2010.8027-1.86750.166115.051-3.14244.36210.091-0.14140.17040.39680.1333-0.5055-0.2325-0.2669-0.22430.11940.0296-0.15770.1915-0.03120.29815.072227.7264-1.7857
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 20
2X-RAY DIFFRACTION2A21 - 29
3X-RAY DIFFRACTION3A30 - 38
4X-RAY DIFFRACTION4A39 - 56
5X-RAY DIFFRACTION5A57 - 76
6X-RAY DIFFRACTION6A77 - 86
7X-RAY DIFFRACTION7A87 - 108
8X-RAY DIFFRACTION8A109 - 125
9X-RAY DIFFRACTION9A126 - 159
10X-RAY DIFFRACTION10A160 - 179
11X-RAY DIFFRACTION11A180 - 187
12X-RAY DIFFRACTION12A188 - 225
13X-RAY DIFFRACTION13A226 - 251
14X-RAY DIFFRACTION14A252 - 257
15X-RAY DIFFRACTION15A258 - 269
16X-RAY DIFFRACTION16A270 - 283
17X-RAY DIFFRACTION17A284 - 293
18X-RAY DIFFRACTION18A294 - 301
19X-RAY DIFFRACTION19A302 - 327
20X-RAY DIFFRACTION20A328 - 349

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