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- PDB-4jvj: Crystal structure of human FPPS in complex with magnesium, CL0113... -

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Basic information

Entry
Database: PDB / ID: 4jvj
TitleCrystal structure of human FPPS in complex with magnesium, CL01131, and sulfate
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 / cytoplasm / cytosol
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-1MV / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.8 Å
AuthorsPark, J. / Leung, C.-Y. / Tsantrizos, Y.S. / Berghuis, A.M.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Thienopyrimidine Bisphosphonate (ThPBP) Inhibitors of the Human Farnesyl Pyrophosphate Synthase: Optimization and Characterization of the Mode of Inhibition.
Authors: Leung, C.Y. / Park, J. / De Schutter, J.W. / Sebag, M. / Berghuis, A.M. / Tsantrizos, Y.S.
History
DepositionMar 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
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

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Assembly

Deposited unit
F: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7296
Polymers43,1451
Non-polymers5845
Water25214
1
F: Farnesyl pyrophosphate synthase
hetero molecules

F: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,45912
Polymers86,2902
Non-polymers1,16910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4870 Å2
ΔGint-120 kcal/mol
Surface area26390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.330, 111.330, 67.462
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 / Fragment: UNP residues 67-419
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-1MV / ({[6-(4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}methanediyl)bis(phosphonic acid)


Mass: 415.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15N3O6P2S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.42 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 8% PEG8000, 0.1 M TRIS, 0.2 M magnesium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 13, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 10724 / Num. obs: 10724 / % possible obs: 98.6 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 27.3
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 6.6 / Num. unique all: 503 / % possible all: 99.6

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Processing

Software
NameVersionClassification
MxDCdata collection
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.7.0029phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 4DEM

4dem


Resolution: 2.8→49.84 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.913 / SU B: 22.028 / SU ML: 0.415 / Cross valid method: THROUGHOUT / ESU R Free: 0.425 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28828 509 4.8 %RANDOM
Rwork0.23584 ---
all0.23845 10170 --
obs0.23845 10170 98.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.717 Å2
Baniso -1Baniso -2Baniso -3
1--7.57 Å2-0 Å2-0 Å2
2---7.57 Å20 Å2
3---15.15 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2648 0 34 14 2696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022739
X-RAY DIFFRACTIONr_bond_other_d0.0020.022521
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9763738
X-RAY DIFFRACTIONr_angle_other_deg0.8183.0015754
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6835342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.99524.667120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.50515421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0951510
X-RAY DIFFRACTIONr_chiral_restr0.0690.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023136
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02631
LS refinement shellResolution: 2.8→2.874 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 35 -
Rwork0.436 686 -
obs-721 93.39 %

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