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- PDB-2f8z: Crystal structure of human FPPS in complex with zoledronate and i... -

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Basic information

Entry
Database: PDB / ID: 2f8z
TitleCrystal structure of human FPPS in complex with zoledronate and isopentenyl diphosphate
ComponentsFarnesyl Diphosphate Synthase
KeywordsTRANSFERASE / Mevalonate pathway / isoprene biosynthesis / cholesterol biosynthesis / bisphosphonate inhibitor
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
3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ZOLEDRONIC ACID / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsRondeau, J.-M. / Bitsch, F. / Bourgier, E. / Geiser, M. / Hemmig, R. / Kroemer, M. / Lehmann, S. / Ramage, P. / Rieffel, S. / Strauss, A. ...Rondeau, J.-M. / Bitsch, F. / Bourgier, E. / Geiser, M. / Hemmig, R. / Kroemer, M. / Lehmann, S. / Ramage, P. / Rieffel, S. / Strauss, A. / Green, J.R. / Jahnke, W.
CitationJournal: Chemmedchem / Year: 2006
Title: Structural basis for the exceptional in vivo efficacy of bisphosphonate drugs.
Authors: Rondeau, J.M. / Bitsch, F. / Bourgier, E. / Geiser, M. / Hemmig, R. / Kroemer, M. / Lehmann, S. / Ramage, P. / Rieffel, S. / Strauss, A. / Green, J.R. / Jahnke, W.
History
DepositionDec 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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_conn.ptnr2_label_seq_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 Diphosphate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7756
Polymers40,1841
Non-polymers5915
Water1,09961
1
F: Farnesyl Diphosphate Synthase
hetero molecules

F: Farnesyl Diphosphate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,55012
Polymers80,3682
Non-polymers1,18210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area7050 Å2
ΔGint-81 kcal/mol
Surface area26930 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)112.155, 112.155, 65.725
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsTHE BIOLOGICAL ASSEMBLY IS A HOMODIMER

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Components

#1: Protein Farnesyl Diphosphate Synthase / E.C.2.5.1.1, E.C.2.5.1.10 / FPP synthetase / FPS / Farnesyl pyrophosphate synthetase


Mass: 40183.855 Da / Num. of mol.: 1 / Fragment: Residues 6-353
Source method: isolated from a genetically manipulated source
Details: Includes: Dimethylallyltranstransferase; Geranyltranstransferase
Source: (gene. exp.) Homo sapiens (human) / Gene: FDPS, FPS, KIAA1293 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 TUNER(DE3)
References: UniProt: P14324, dimethylallyltranstransferase, (2E,6E)-farnesyl diphosphate synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE / Isopentenyl pyrophosphate


Mass: 246.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O7P2
#4: Chemical ChemComp-ZOL / ZOLEDRONIC ACID / (1-HYDROXY-2-IMIDAZOL-1-YLETHYLIDENE)DIPHOSPHONIC ACID / Zoledronic acid


Mass: 272.090 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N2O7P2 / Comment: medication*YM
#5: 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: 2.57 Å3/Da / Density % sol: 52.16 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 1.2M sodium potassium phosphate, 25% glycerol, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00033 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 29, 2004
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00033 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. all: 13248 / Num. obs: 13248 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 62.5 Å2 / Rmerge(I) obs: 0.072 / Χ2: 1.035 / Net I/σ(I): 8.8
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.481 / Num. unique all: 1282 / Χ2: 0.649 / % possible all: 99.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNX2002refinement
CNX2002phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2F8C

2f8c


Resolution: 2.6→56.71 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 18221610 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1358 10.3 %RANDOM
Rwork0.22 ---
all0.226 13212 --
obs0.226 13212 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.171 Å2 / ksol: 0.368 e/Å3
Displacement parametersBiso mean: 59.9 Å2
Baniso -1Baniso -2Baniso -3
1--20.79 Å20 Å20 Å2
2---20.79 Å20 Å2
3---41.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.68 Å0.64 Å
Refinement stepCycle: LAST / Resolution: 2.6→56.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2806 0 33 61 2900
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_d1.2
X-RAY DIFFRACTIONx_dihedral_angle_d21.3
X-RAY DIFFRACTIONx_improper_angle_d0.74
X-RAY DIFFRACTIONx_mcbond_it3.371.5
X-RAY DIFFRACTIONx_mcangle_it5.172
X-RAY DIFFRACTIONx_scbond_it5.312
X-RAY DIFFRACTIONx_scangle_it7.362.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.486 187 9.4 %
Rwork0.426 1811 -
obs-1998 92 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.topprotein_rep.param
X-RAY DIFFRACTION2zometa.prm
X-RAY DIFFRACTION3water.topwater_rep.param
X-RAY DIFFRACTION4ion.topion.param
X-RAY DIFFRACTION5ipp.prm

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