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

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Basic information

Entry
Database: PDB / ID: 4nua
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 synthase
KeywordsTRANSFERASE / Cholesterol Synthesis / Alpha-Helical Prenyltransferase Fold / Isoprene Synthesis / Lipid Synthesis / Steroid Biosynthesis / Isoprenoid Pathway / Dimethylallyl Pyrophosphate / Isopentenyl Pyrophosphate
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
PHOSPHATE ION / Chem-RIS / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 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
DepositionDec 3, 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 / _chem_comp.pdbx_synonyms / _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)43,89412
Polymers43,0711
Non-polymers82311
Water6,936385
1
A: Farnesyl pyrophosphate synthase
hetero molecules

A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,78924
Polymers86,1422
Non-polymers1,64722
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7440 Å2
ΔGint-53 kcal/mol
Surface area27050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.290, 111.290, 66.870
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-1382-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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: 43070.859 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, 396 molecules

#2: Chemical ChemComp-RIS / 1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID / Risedronate


Mass: 283.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11NO7P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M NH4Cl, PEG6000, 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: 1.43→42.77 Å / Num. all: 77686 / Num. obs: 77586 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.8 % / Biso Wilson estimate: 19.74 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 15.7
Reflection shellResolution: 1.43→1.51 Å / % possible all: 99.6

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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: 1.43→20.94 Å / Cor.coef. Fo:Fc: 0.9668 / Cor.coef. Fo:Fc free: 0.9528 / SU R Cruickshank DPI: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1807 3901 5.03 %RANDOM
Rwork0.1614 ---
obs0.1624 77586 99.82 %-
all-77686 --
Displacement parametersBiso mean: 26.11 Å2
Baniso -1Baniso -2Baniso -3
1-1.2696 Å20 Å20 Å2
2--1.2696 Å20 Å2
3----2.5392 Å2
Refine analyzeLuzzati coordinate error obs: 0.158 Å
Refinement stepCycle: LAST / Resolution: 1.43→20.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2695 0 49 385 3129
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0153048HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.184169HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1467SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes81HARMONIC2
X-RAY DIFFRACTIONt_gen_planes461HARMONIC5
X-RAY DIFFRACTIONt_it3048HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.11
X-RAY DIFFRACTIONt_other_torsion2.56
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion385SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4219SEMIHARMONIC4
LS refinement shellResolution: 1.43→1.47 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2517 268 4.79 %
Rwork0.2347 5332 -
all0.2355 5600 -
obs--99.82 %
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)
11.1574-1.79631.58651.8781-0.29750.67550.1113-0.2224-0.01140.1087-0.15070.0425-0.2439-0.16760.0394-0.07520.09380.04620.12-0.0131-0.0612-0.330129.50369.3526
21.74980.8873-1.09850.5491-0.35044.1955-0.0176-0.23480.00480.1387-0.03080.03890.0351-0.02570.0484-0.02740.00720.01160.0507-0.009-0.05615.726225.922315.7204
32.64250.08530.58821.01380.56281.0492-0.058-0.27290.0479-0.01150.05470.1231-0.0192-0.2260.0034-0.07570.0107-0.00230.04970.0273-0.0059-6.680725.19570.6291
41.04970.41190.09460.6402-0.17490.5246-0.0019-0.17680.00050.04920.01440.0316-0.0164-0.1098-0.0125-0.03310.00450.00070.00790.0114-0.019510.944424.97994.2005
51.18750.6729-0.44011.4758-0.97541.2308-0.06580.0424-0.0557-0.17090.01910.03930.09630.01490.0467-0.00580.0008-0.0308-0.022-0.0005-0.016515.104424.3921-13.8852
60.90660.14730.12190.16110.04660.3059-0.00990.00470.0873-0.05960.01120.12420.0084-0.0513-0.0012-0.0233-0.0033-0.0235-0.01540.0110.00037.073130.7728-11.9959
72.7232-0.14061.19861.675-0.07613.41020.00360.54420.282-0.22950.13040.0099-0.01080.3274-0.134-0.0286-0.0271-0.00250.04620.0679-0.056522.974143.5988-24.716
81.98750.43980.49490.95960.35040.3878-0.00720.2140.4056-0.0414-0.00370.1781-0.05790.03270.011-0.0296-0.0036-0.038-0.0070.06730.00228.283142.162-21.3458
93.0861-0.127-0.7920.003-2.24441.62980.0489-0.11060.00640.01750.13510.0956-0.13210.0413-0.184-0.03240.0008-0.01890.0113-0.01080.0031-6.889130.3222-12.1663
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|9 - A|28 }A9 - 28
2X-RAY DIFFRACTION2{ A|29 - A|52 }A29 - 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|206 }A153 - 206
6X-RAY DIFFRACTION6{ A|207 - A|268 }A207 - 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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