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- PDB-4dem: Crystal structure of human FPPS in complex with YS_04_70 -

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Basic information

Entry
Database: PDB / ID: 4dem
TitleCrystal structure of human FPPS in complex with YS_04_70
ComponentsFarnesyl pyrophosphate synthase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / MEVALONATE PATHWAY / ISOPRENE BIOSYNTHESIS / CHOLESTEROL BIOSYNTHESIS / BISPHOSPHONATE / TRANSFERASE / 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-YS4 / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPark, J. / Lin, Y.-S. / Tsantrizos, Y.S. / Berghuis, A.M.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Design and Synthesis of Active Site Inhibitors of the Human Farnesyl Pyrophosphate Synthase: Apoptosis and Inhibition of ERK Phosphorylation in Multiple Myeloma Cells.
Authors: Lin, Y.S. / Park, J. / De Schutter, J.W. / Huang, X.F. / Berghuis, A.M. / Sebag, M. / Tsantrizos, Y.S.
History
DepositionJan 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Sep 13, 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)43,6205
Polymers43,1451
Non-polymers4754
Water3,981221
1
F: Farnesyl pyrophosphate synthase
hetero molecules

F: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,24010
Polymers86,2902
Non-polymers9508
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4700 Å2
ΔGint-83 kcal/mol
Surface area26710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.230, 111.230, 67.724
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-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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.43 Å3/Da / Density % sol: 49.33 %
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 295K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 13, 2011
RadiationMonochromator: ACCEL DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 36881 / Num. obs: 36881 / % possible obs: 99.9 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 50.4
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 14 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 8 / Num. unique all: 1816 / Rsym value: 0.391 / % possible all: 100

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Processing

Software
NameVersionClassification
MxDCdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3N46

3n46


Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.688 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20176 1837 5 %RANDOM
Rwork0.17409 ---
all0.17545 34866 --
obs0.17545 34866 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.781 Å2
Baniso -1Baniso -2Baniso -3
1--1.72 Å20 Å20 Å2
2---1.72 Å20 Å2
3---3.43 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2742 0 29 221 2992
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222893
X-RAY DIFFRACTIONr_bond_other_d0.0010.021935
X-RAY DIFFRACTIONr_angle_refined_deg1.7491.9793941
X-RAY DIFFRACTIONr_angle_other_deg1.1113.0024730
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9455363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.48624.526137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82315494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3711515
X-RAY DIFFRACTIONr_chiral_restr0.1290.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023236
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02598
X-RAY DIFFRACTIONr_mcbond_it1.3811.51749
X-RAY DIFFRACTIONr_mcbond_other0.4251.5707
X-RAY DIFFRACTIONr_mcangle_it2.34222818
X-RAY DIFFRACTIONr_scbond_it3.49531144
X-RAY DIFFRACTIONr_scangle_it5.5494.51114
LS refinement shellResolution: 1.85→1.896 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 131 -
Rwork0.211 2476 -
obs-2607 97.6 %
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)
17.7993-6.30999.2375.3066-4.280311.8861-0.0254-0.75280.1440.0114-0.0774-0.1584-0.2213-1.04750.10280.03530.11610.0860.4625-0.08150.1137-0.925629.43948.7619
21.3676-0.5063-0.09770.9125-1.31821.5228-0.0986-0.2670.11110.06340.22180.0688-0.0289-0.2001-0.12320.21490.03260.01530.2758-0.02140.139515.405724.155416.8627
33.1147-0.4960.3156-0.18650.0169-0.41450.04630.00090.2413-0.0179-0.03740.00890.0188-0.0826-0.00890.1076-0.0081-0.01250.27320.0220.2564-6.323425.32830.292
40.68330.22530.09810.2505-0.13680.1145-0.0222-0.0821-0.00210.03730.0457-0.0531-0.045-0.097-0.02350.18370.0005-0.00120.2191-0.0010.22611.50925.46413.9515
50.63270.7014-0.231.4215-1.13980.74160.07460.0566-0.0708-0.0136-0.00830.0351-0.00740.0117-0.06630.19640.001-0.00710.19690.00040.229312.29718.1599-7.8527
60.80970.19950.00130.1588-0.01090.0660.02170.10930.1104-0.0536-0.00570.0940.02670.017-0.01610.17590.0021-0.02930.23010.03090.214313.327833.3387-16.7113
71.90490.5610.24570.74560.660.30260.19940.17590.2903-0.0044-0.17180.03410.0158-0.0923-0.02760.11630.0013-0.0510.19910.14450.26118.117142.0628-20.8611
83.33940.42841.17250.5888-0.3822-0.25590.04540.03240.17570.08930.00750.1609-0.0254-0.0542-0.05290.16470.0016-0.02560.2188-0.01860.2401-5.834931.7565-11.9648
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1F22 - 42
2X-RAY DIFFRACTION2F43 - 66
3X-RAY DIFFRACTION3F67 - 92
4X-RAY DIFFRACTION4F93 - 166
5X-RAY DIFFRACTION5F167 - 190
6X-RAY DIFFRACTION6F191 - 308
7X-RAY DIFFRACTION7F309 - 346
8X-RAY DIFFRACTION8F347 - 367

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