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- PDB-4kq5: Crystal Structure of Human Farnesyl Pyrophosphate Synthase Mutant... -

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Basic information

Entry
Database: PDB / ID: 4kq5
TitleCrystal Structure of Human Farnesyl Pyrophosphate Synthase Mutant (Y204A) Complexed with Mg and Zoledronate
ComponentsFarnesyl pyrophosphate synthaseDimethylallyltranstransferase
KeywordsTRANSFERASE / Isoprene biosynthesis / Lipid synthesis / steroid biosynthesis / dimethylallyl pyrophosphate / 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
ZOLEDRONIC ACID / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBarnett, B.L. / Tsoumpra, M.K. / Muniz, J.R.C.
CitationJournal: To be Published
Title: Crystal Structure of Human Farnesyl Pyrophosphate Synthase Mutant (Y204A) Complexed with Mg and Zoledronate
Authors: Tsoumpra, M.K. / Muniz, J.R.C. / Barnett, B.L. / Pilka, E. / Kwaasi, A. / Kavanagh, K.L. / Evdokimov, A.G. / Walter, R.L. / Ebetino, F.H. / Oppermann, U. / Russell, R.G.G. / Dunford, J.E.
History
DepositionMay 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 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)43,4606
Polymers43,0531
Non-polymers4075
Water3,189177
1
A: Farnesyl pyrophosphate synthase
hetero molecules

A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,92012
Polymers86,1062
Non-polymers81410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6390 Å2
ΔGint-79 kcal/mol
Surface area27400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.650, 111.650, 67.940
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

21A-653-

HOH

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Components

#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: 43052.887 Da / Num. of mol.: 1 / Fragment: UNP residues 67-419 / Mutation: Y204A
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
#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M NH4Cl, 20% 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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 3, 2011
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→32.64 Å / Num. all: 17364 / Num. obs: 17364 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 46.76 Å2 / Rmerge(I) obs: 0.113 / Rsym value: 0.113 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.4-2.536.10.6482199.9
2.53-32.646.50.11310.21100

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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: 2.4→32.5 Å / Cor.coef. Fo:Fc: 0.9446 / Cor.coef. Fo:Fc free: 0.9173 / SU R Cruickshank DPI: 0.327 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 877 5.06 %RANDOM
Rwork0.1852 ---
obs0.1882 17315 99.92 %-
all-17364 --
Displacement parametersBiso mean: 56.54 Å2
Baniso -1Baniso -2Baniso -3
1-7.8627 Å20 Å20 Å2
2--7.8627 Å20 Å2
3----15.7254 Å2
Refine analyzeLuzzati coordinate error obs: 0.344 Å
Refinement stepCycle: LAST / Resolution: 2.4→32.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2723 0 23 177 2923
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012852HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.973878HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1343SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes81HARMONIC2
X-RAY DIFFRACTIONt_gen_planes411HARMONIC5
X-RAY DIFFRACTIONt_it2852HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.51
X-RAY DIFFRACTIONt_other_torsion3.04
X-RAY DIFFRACTIONt_chiral_improper_torsion360SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3535SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.54 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2769 176 6.41 %
Rwork0.2209 2569 -
all0.2245 2745 -
obs--99.92 %
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)
12.7354-0.252-1.99732.89140.637600.0346-0.01390.09620.0371-0.08050.0338-0.2817-0.27880.0459-0.29550.14340.0403-0.055-0.14870.2899-0.90130.37739.2918
23.3998-0.99670.23720.5228-2.45251.7134-0.041-0.3953-0.04140.1924-0.0790.22420.1728-0.15120.12-0.215-0.0040.0047-0.17-0.09550.30415.51124.277616.7165
34.1005-2.1269-0.67171.41910.07763.32660.0092-0.14470.03-0.0675-0.0250.14350.1288-0.12280.0158-0.29010.0563-0.0112-0.1080.04630.3034-5.775125.89280.1402
42.9967-0.3221-0.03780.55290.14060.6387-0.0587-0.1610.36410.054-0.0246-0.1532-0.0694-0.1870.0833-0.27530.0531-0.0463-0.2563-0.06810.300211.959230.13592.7834
51.13130.17520.19280.2857-0.21160.49970.0089-0.3321-0.01750.1015-0.05550.07590.0907-0.20690.0466-0.24810.0031-0.0121-0.1844-0.01070.30410.351417.77236.188
60.3946-0.08851.5861.03270.227100.0073-0.00870.182-0.239-0.0804-0.0440.2054-0.10810.073-0.20380.03660.0043-0.24390.0010.289713.210919.0372-8.3431
71.70330.948-1.73573.6051-1.10390.63580.0778-0.0096-0.0683-0.5291-0.0612-0.22910.0691-0.0231-0.0165-0.21950.0111-0.0184-0.21110.03910.30118.01730.017-18.9842
83.171.1128-0.27281.8751-0.39981.23220.02610.17760.2739-0.11760.0330.2226-0.0458-0.1152-0.059-0.28270.0641-0.0473-0.24580.01780.30157.221931.1371-11.9816
92.59621.4267-2.83893.20780.79160.2521-0.04860.2150.0924-0.24730.2953-0.12590.00340.1376-0.2467-0.2176-0.01970.0511-0.22710.07110.30423.500443.749-24.6766
100.1194-1.04620.57890.4040.95711.10090.0780.2860.2592-0.3537-0.0928-0.039-0.194-0.09340.0147-0.22730.0299-0.0467-0.23130.12510.30288.196241.9449-21.4011
113.8724-2.761-1.17160.60290.65680.7221-0.00260.05960.0136-0.04860.00370.0064-0.1497-0.0996-0.0011-0.2679-0.0025-0.0804-0.17050.00890.3033-6.597130.4205-12.3664
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|9 - 28}A9 - 28
2X-RAY DIFFRACTION2{A|29 - 52}A29 - 52
3X-RAY DIFFRACTION3{A|53 - 78}A53 - 78
4X-RAY DIFFRACTION4{A|79 - 124}A79 - 124
5X-RAY DIFFRACTION5{A|125 - 152}A125 - 152
6X-RAY DIFFRACTION6{A|153 - 177}A153 - 177
7X-RAY DIFFRACTION7{A|178 - 206}A178 - 206
8X-RAY DIFFRACTION8{A|207 - 268}A207 - 268
9X-RAY DIFFRACTION9{A|269 - 294}A269 - 294
10X-RAY DIFFRACTION10{A|295 - 332}A295 - 332
11X-RAY DIFFRACTION11{A|333 - 350}A333 - 350

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