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- PDB-4xqt: Crystal structure of human FPPS in complex with three magnesium ions -

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Basic information

Entry
Database: PDB / ID: 4xqt
TitleCrystal structure of human FPPS in complex with three magnesium ions
ComponentsFarnesyl pyrophosphate synthase
KeywordsTRANSFERASE
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
Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsPark, J. / Berghuis, A.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Fonds de recherche Nature et technologies Canada
CitationJournal: To Be Published
Title: Crystal structure of human FPPS in complex with three magnesium ions
Authors: Park, J. / Berghuis, A.M.
History
DepositionJan 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_struct_oper_list / struct_conn
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_alt_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_alt_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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4106
Polymers43,1451
Non-polymers2655
Water1,18966
1
F: Farnesyl pyrophosphate synthase
hetero molecules

F: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,82012
Polymers86,2902
Non-polymers53010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area5400 Å2
ΔGint-128 kcal/mol
Surface area27990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.340, 110.340, 78.520
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 / FPS / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl ...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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.77 Å3/Da / Density % sol: 55.59 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.36 M magnesium sulfate, 15% glycerol, 0.085 M MES

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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: May 29, 2013
RadiationMonochromator: ACCEL/Bruker 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: 2.1→45.14 Å / Num. obs: 28729 / % possible obs: 99.7 % / Redundancy: 8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 26.6
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 7 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 2.4 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0073phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2F7M

2f7m


Resolution: 2.1→45.14 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 14.589 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22684 1437 5 %RANDOM
Rwork0.19104 ---
obs0.19292 27256 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.379 Å2
Baniso -1Baniso -2Baniso -3
1--4.47 Å20 Å20 Å2
2---4.47 Å20 Å2
3---8.94 Å2
Refinement stepCycle: 1 / Resolution: 2.1→45.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2632 0 13 66 2711
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192711
X-RAY DIFFRACTIONr_bond_other_d0.0010.022523
X-RAY DIFFRACTIONr_angle_refined_deg1.7851.9683691
X-RAY DIFFRACTIONr_angle_other_deg0.89235766
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8735340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57624.417120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04815431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7191512
X-RAY DIFFRACTIONr_chiral_restr0.1010.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023094
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02626
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_it2.8763.5851360
X-RAY DIFFRACTIONr_mcbond_other2.8743.5841359
X-RAY DIFFRACTIONr_mcangle_it4.0495.3671700
X-RAY DIFFRACTIONr_mcangle_other4.0485.3681701
X-RAY DIFFRACTIONr_scbond_it3.763.7541351
X-RAY DIFFRACTIONr_scbond_other3.5253.7231340
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9475.4961974
X-RAY DIFFRACTIONr_long_range_B_refined7.73129.3773297
X-RAY DIFFRACTIONr_long_range_B_other7.72129.133270
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.102→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 109 -
Rwork0.335 1965 -
obs--99.19 %
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)
112.54364.719-2.08597.838-3.01026.2144-0.24170.24920.18660.07510.44610.45640.3741-0.7478-0.20440.3746-0.0798-0.09070.3832-0.06780.19861.527880.604310.6071
28.82381.3672-0.68750.2309-0.12960.08250.1232-0.10281.0363-0.01370.02320.22120.0521-0.0422-0.14650.5495-0.02440.04650.4624-0.00920.400813.309591.8261-2.5215
35.6247-0.2379-3.4472.7594-0.00764.5129-0.01440.5952-0.3943-0.40230.07620.67820.163-0.6644-0.06180.1903-0.085-0.11260.28040.0140.21612.986583.845114.8755
47.6892-2.8137-0.02475.0358-0.76211.3433-0.08180.1087-0.3545-0.25910.0290.07120.2688-0.14630.05280.186-0.03660.01270.1022-0.01480.018817.776980.729816.6052
58.9991-4.51854.5394.6666-3.28724.72750.0081-0.1372-0.07760.04680.07840.1551-0.0808-0.0377-0.08650.1168-0.04110.06150.1666-0.00720.083511.995792.184725.9469
60.41790.03610.17080.00880.01630.07030.01360.1712-0.1925-0.02410.05690.00710.00170.0838-0.07050.54130.0648-0.01860.54020.08180.440530.571474.259339.5493
77.7446-2.28822.00224.6183-2.50854.432-0.0661-0.44720.28910.4456-0.0333-0.0379-0.10610.12590.09940.1371-0.03870.03840.2445-0.0090.02748.868786.328134.6871
84.6147-2.42240.17367.0259-2.36752.5002-0.0824-0.4052-0.64280.0138-0.2137-0.17350.42450.38580.29610.27280.03890.09340.41650.12420.159712.099372.635939.0879
93.42041.99170.65352.26822.87577.5569-0.1894-0.1625-0.40780.28380.1949-0.56910.30351.2698-0.00550.63320.2257-0.0390.91210.39810.837627.632162.969643.7254
106.9407-3.58841.65384.405-2.31682.03880.0849-0.2934-0.30150.053-0.1130.11280.43710.10380.02810.33050.01010.06980.34020.03630.15852.438674.310141.8851
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1F11 - 29
2X-RAY DIFFRACTION2F30 - 36
3X-RAY DIFFRACTION3F37 - 93
4X-RAY DIFFRACTION4F94 - 147
5X-RAY DIFFRACTION5F148 - 178
6X-RAY DIFFRACTION6F179 - 185
7X-RAY DIFFRACTION7F186 - 224
8X-RAY DIFFRACTION8F225 - 280
9X-RAY DIFFRACTION9F281 - 298
10X-RAY DIFFRACTION10F299 - 349

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