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- PDB-4nkf: The effects of Lysine 200 and Phenylalanine 239 Farnesyl Pyrophos... -

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Basic information

Entry
Database: PDB / ID: 4nkf
TitleThe effects of Lysine 200 and Phenylalanine 239 Farnesyl Pyrophosphate Synthase (FPPS) mutations on the catalytic activity, crystal structure and inhibition by nitrogen containing bisphosphonates
ComponentsFarnesyl pyrophosphate synthaseDimethylallyltranstransferase
KeywordsTRANSFERASE / Alpha-Helical Prenyltransferase / Isoprene Biosynthesis / Lipid Synthesis / Steroid Biosynthesis / Isoprenoid Pathway / Cholesterol Synthesis / Bisphosphonates
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
PAMIDRONATE / DI(HYDROXYETHYL)ETHER / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTsoumpra, M.K. / Barnett, B.L. / Muniz, J.R.C. / Walter, R.L. / Ebetino, F.H. / von Delft, F. / Russell, R.G.G. / Oppermann, U. / Dunford, J.E.
CitationJournal: To be Published
Title: The effects of Lysine 200 and Phenylalanine 239 Farnesyl Pyrophosphate Synthase (FPPS) mutations on the catalytic activity, crystal structure and inhibition by nitrogen containing bisphosphonates
Authors: Tsoumpra, M.K. / Barnett, B.L. / Muniz, J.R.C. / Walter, R.L. / Ebetino, F.H. / von Delft, F. / Russell, R.G.G. / Oppermann, U. / Dunford, J.E.
History
DepositionNov 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
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

Downloads & links

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Assembly

Deposited unit
A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5757
Polymers43,0991
Non-polymers4766
Water2,972165
1
A: Farnesyl pyrophosphate synthase
hetero molecules

A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,15014
Polymers86,1982
Non-polymers95212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7110 Å2
ΔGint-69 kcal/mol
Surface area26880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.450, 111.450, 67.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-649-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 43098.914 Da / Num. of mol.: 1 / Fragment: UNP residues 67-419 / Mutation: F239A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FDPS, FPS, KIAA1293 / Plasmid: PET 11 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P14324, (2E,6E)-farnesyl diphosphate synthase, dimethylallyltranstransferase

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Non-polymers , 5 types, 171 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-210 / PAMIDRONATE / (3-AMINO-1-HYDROXY-1-PHOSPHONO-PROPYL)PHOSPHONIC ACID / Pamidronic acid


Mass: 235.069 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H11NO7P2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 49.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M NH4Cl, 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: Diamond / Beamline: I02 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2009
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2→42.98 Å / Num. all: 29260 / Num. obs: 29167 / % possible obs: 99.8 % / Observed criterion σ(F): 2.7 / Observed criterion σ(I): 2.7 / Redundancy: 10.6 % / Biso Wilson estimate: 36.17 Å2 / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 12.3
Reflection shellResolution: 2→2.21 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CP6

3cp6


Resolution: 2→17.23 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.9477 / SU R Cruickshank DPI: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2014 1481 5.08 %RANDOM
Rwork0.1775 ---
all0.1787 ---
obs0.1787 29167 99.75 %-
Displacement parametersBiso mean: 48.84 Å2
Baniso -1Baniso -2Baniso -3
1-2.5931 Å20 Å20 Å2
2--2.5931 Å20 Å2
3----5.1861 Å2
Refine analyzeLuzzati coordinate error obs: 0.251 Å
Refinement stepCycle: LAST / Resolution: 2→17.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2690 0 27 165 2882
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012817HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.93826HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1318SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes72HARMONIC2
X-RAY DIFFRACTIONt_gen_planes404HARMONIC5
X-RAY DIFFRACTIONt_it2817HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.73
X-RAY DIFFRACTIONt_other_torsion2.94
X-RAY DIFFRACTIONt_chiral_improper_torsion358SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3485SEMIHARMONIC4
LS refinement shellResolution: 2→2.07 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2533 133 4.7 %
Rwork0.2157 2697 -
all0.2175 2830 -
obs--99.75 %
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)
12.3535-0.11980.17353.81680.29781.91770.0863-0.14040.06630.1179-0.13540.0863-0.2148-0.28650.0491-0.26240.14630.14640.0109-0.08030.1799-0.535230.3578.3078
20.4615-0.11060.67651.2372-1.72864.1422-0.0239-0.2671-0.02810.1385-0.07940.18340.1208-0.02630.1033-0.20890.03430.0785-0.1134-0.03170.234416.228825.516715.9432
34.11990.09960.37461.02120.93632.86480.0083-0.2199-0.013-0.0244-0.01540.1615-0.0016-0.44480.007-0.20740.07890.00530.01270.01210.2901-6.035225.7910.2769
42.79150.85580.44831.83390.16491.48280.089-0.35710.01650.1324-0.02850.0575-0.0013-0.2227-0.0605-0.18030.03290.0023-0.1526-0.00870.166511.345725.44644.1038
53.16971.2128-1.13750.8395-1.45542.773-0.00980.0344-0.1631-0.08190.06920.18320.1775-0.0791-0.0593-0.15930.0537-0.0447-0.1588-0.03010.259913.057718.8801-8.5204
61.93570.4382-0.07371.0093-0.07950.8128-0.04820.12030.0951-0.14490.01510.16980.0283-0.01420.0331-0.17050.023-0.0631-0.101-0.00990.191810.361530.415-14.3282
71.77420.12930.78041.57020.81231.34160.04220.43330.3117-0.20220.1724-0.1019-0.10580.2332-0.2146-0.1338-0.0599-0.00030.01240.08030.164823.435343.5694-24.7685
82.63661.03090.43271.33230.43710.82970.08910.37610.413-0.2383-0.07130.008-0.17370.0378-0.0178-0.1860.0299-0.0604-0.12750.07080.27957.69341.5671-21.6073
94.125-1.5247-1.64470-0.68043.1197-0.0102-0.1079-0.04410.10640.15220.127-0.12110.0335-0.142-0.27890.0468-0.0705-0.0859-0.07750.2812-6.733130.3323-12.4416
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|8 - A|29 }A8 - 29
2X-RAY DIFFRACTION2{ A|30 - A|52 }A30 - 52
3X-RAY DIFFRACTION3{ A|53 - A|78 }A53 - 78
4X-RAY DIFFRACTION4{ A|79 - A|152 }A79 - 152
5X-RAY DIFFRACTION5{ A|153 - A|177 }A153 - 177
6X-RAY DIFFRACTION6{ A|178 - A|268 }A178 - 268
7X-RAY DIFFRACTION7{ A|269 - A|294 }A269 - 294
8X-RAY DIFFRACTION8{ A|295 - A|332 }A295 - 332
9X-RAY DIFFRACTION9{ A|333 - A|350 }A333 - 350

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