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- PDB-3cp6: Crystal structure of human farnesyl diphosphate synthase (T201A m... -

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Basic information

Entry
Database: PDB / ID: 3cp6
TitleCrystal structure of human farnesyl diphosphate synthase (T201A mutant) complexed with Mg and biphosphonate inhibitor
ComponentsFarnesyl pyrophosphate synthetase
KeywordsTRANSFERASE / ISOPRENOID PATHWAY / CHOLESTEROL SYNTHESIS / BISPHOSPHONATE / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / CHOLESTEROL BIOSYNTHESIS / HOST-VIRUS INTERACTION ISOPRENE BIOSYNTHESIS / LIPID SYNTHESIS / STEROID BIOSYNTHESIS / STEROL BIOSYNTHESIS
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-RSX / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPilka, E.S. / Dunford, J.E. / Guo, K. / Pike, A.C.W. / von Delft, F. / Barnett, B.L. / Ebetino, F.H. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. ...Pilka, E.S. / Dunford, J.E. / Guo, K. / Pike, A.C.W. / von Delft, F. / Barnett, B.L. / Ebetino, F.H. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Russell, R.G.G. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Human farnesyl diphosphate synthase (T201A mutant) complexed with Mg and biphosphonate inhibitor.
Authors: Pilka, E.S. / Dunford, J.E. / Guo, K. / Pike, A.C.W. / von Delft, F. / Barnett, B.L. / Ebetino, F.H. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Russell, R.G.G. / Oppermann, U.
History
DepositionMar 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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.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.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.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
Revision 1.4Feb 1, 2023Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Farnesyl pyrophosphate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6045
Polymers43,2461
Non-polymers3584
Water3,783210
1
A: Farnesyl pyrophosphate synthetase
hetero molecules

A: Farnesyl pyrophosphate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,20810
Polymers86,4922
Non-polymers7168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3940 Å2
ΔGint-25.6 kcal/mol
Surface area26900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.531, 112.531, 62.919
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 synthetase / (FPP synthetase) (FPS) (Farnesyl diphosphate synthetase) [Includes: Dimethylallyltranstransferase ...(FPP synthetase) (FPS) (Farnesyl diphosphate synthetase) [Includes: Dimethylallyltranstransferase (EC 2.5.1.1) / Geranyltranstransferase (EC 2.5.1.10)]


Mass: 43246.152 Da / Num. of mol.: 1 / Mutation: T201A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FDPS, FPS, KIAA1293 / Plasmid: pET11 derivative / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(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-RSX / (4aS,7aR)-octahydro-1H-cyclopenta[b]pyridine-6,6-diylbis(phosphonic acid)


Mass: 285.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO6P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M NH4Cl, 20% PEG 6000, 10% Ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 8, 2007
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→29.26 Å / Num. all: 30040 / Num. obs: 28451 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.114 / Rsym value: 0.122 / Net I/σ(I): 9.7
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4311 / Rsym value: 0.658 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QIS

2qis


Resolution: 1.95→27.46 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.507 / SU ML: 0.134 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24321 1547 5.2 %RANDOM
Rwork0.1948 ---
all0.19725 28451 --
obs0.19725 28451 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.284 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å20 Å20 Å2
2---1.8 Å20 Å2
3---3.6 Å2
Refinement stepCycle: LAST / Resolution: 1.95→27.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2639 0 20 210 2869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222748
X-RAY DIFFRACTIONr_bond_other_d0.0010.021825
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.9713741
X-RAY DIFFRACTIONr_angle_other_deg0.97934451
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7975334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57124.552134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02815454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5381515
X-RAY DIFFRACTIONr_chiral_restr0.0770.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023057
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02565
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.38531668
X-RAY DIFFRACTIONr_mcbond_other0.7143674
X-RAY DIFFRACTIONr_mcangle_it3.54852676
X-RAY DIFFRACTIONr_scbond_it6.12181080
X-RAY DIFFRACTIONr_scangle_it8.54111064
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 111 -
Rwork0.298 2059 -
obs--99.95 %
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)
12.83631.63280.46331.25530.36472.5927-0.0121-0.2405-0.19190.3585-0.2760.24360.2804-0.66610.2881-0.0549-0.06760.13810.2598-0.19370.09348.902327.274213.6747
23.04681.44790.90644.1016-1.05323.15340.1096-0.53670.73390.1216-0.15620.5324-0.0559-0.31150.0466-0.06720.00050.05730.0474-0.14780.2773-5.433124.77973.6165
32.10430.44720.68731.9126-0.25571.05340.113-0.19360.103-0.0154-0.0470.10840.1301-0.0509-0.0660.08540.00690.00140.0746-0.04520.078315.359625.2965-0.8913
41.12290.35780.05381.051-0.53890.87610.06180.20250.1971-0.1560.02120.04370.04390.0781-0.0830.03180.032-0.00220.02510.01170.123613.796436.4026-17.8616
52.9627-0.205-1.1552.3266-1.65934.56850.1456-0.08070.11490.14760.0621-0.1803-0.19250.077-0.20770.00010.0171-0.11750.06130.01030.1871-6.382929.3351-16.4115
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA11 - 5234 - 75
2X-RAY DIFFRACTION2AA53 - 8676 - 109
3X-RAY DIFFRACTION3AA87 - 184110 - 207
4X-RAY DIFFRACTION4AA185 - 321208 - 344
5X-RAY DIFFRACTION5AA322 - 348345 - 371

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