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- PDB-3wef: Crystal structure of the human squalene synthase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3wef
TitleCrystal structure of the human squalene synthase in complex with farnesyl thiopyrophosphate
ComponentsSqualene synthase
KeywordsTRANSFERASE / Farnesyl-diphosphate farnesyltransferase / Head-to-head synthases / Cholesterol biosynthesis / Oxidoreductase
Function / homology
Function and homology information


squalene synthase / farnesyl diphosphate metabolic process / squalene synthase [NAD(P)H] activity / Cholesterol biosynthesis / steroid biosynthetic process / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / PPARA activates gene expression / endoplasmic reticulum membrane / endoplasmic reticulum ...squalene synthase / farnesyl diphosphate metabolic process / squalene synthase [NAD(P)H] activity / Cholesterol biosynthesis / steroid biosynthetic process / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / PPARA activates gene expression / endoplasmic reticulum membrane / endoplasmic reticulum / metal ion binding / membrane
Similarity search - Function
Squalene synthase-like / Trans-isoprenyl diphosphate synthases, eukaryotic-type / Squalene and phytoene synthases signature 2. / Squalene/phytoene synthase, conserved site / Squalene and phytoene synthases signature 1. / Trans-isoprenyl diphosphate synthases, head-to-head / Squalene/phytoene synthase / Squalene/phytoene synthase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase ...Squalene synthase-like / Trans-isoprenyl diphosphate synthases, eukaryotic-type / Squalene and phytoene synthases signature 2. / Squalene/phytoene synthase, conserved site / Squalene and phytoene synthases signature 1. / Trans-isoprenyl diphosphate synthases, head-to-head / Squalene/phytoene synthase / Squalene/phytoene synthase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-FPS / Squalene synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsLiu, C.I. / Jeng, W.Y. / Wang, A.H.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural insights into the catalytic mechanism of human squalene synthase.
Authors: Liu, C.I. / Jeng, W.Y. / Chang, W.J. / Shih, M.F. / Ko, T.P. / Wang, A.H.J.
History
DepositionJul 7, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Squalene synthase
B: Squalene synthase
C: Squalene synthase
D: Squalene synthase
E: Squalene synthase
F: Squalene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,88114
Polymers236,6946
Non-polymers3,1878
Water6,341352
1
A: Squalene synthase
B: Squalene synthase
C: Squalene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,3398
Polymers118,3473
Non-polymers1,9925
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10060 Å2
ΔGint-58 kcal/mol
Surface area38210 Å2
MethodPISA
2
D: Squalene synthase
E: Squalene synthase
F: Squalene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,5426
Polymers118,3473
Non-polymers1,1953
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint-43 kcal/mol
Surface area39140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.888, 153.752, 91.613
Angle α, β, γ (deg.)90.00, 91.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Squalene synthase / SQS / SS / FPP:FPP farnesyltransferase / Farnesyl-diphosphate farnesyltransferase


Mass: 39448.969 Da / Num. of mol.: 6 / Fragment: UNP residues 31-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FDFT1 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE3) / References: UniProt: P37268, squalene synthase
#2: Chemical
ChemComp-FPS / S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE / FARNESYL THIOPYROPHOSPHATE


Mass: 398.392 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C15H28O6P2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.56 Å3/Da / Density % sol: 51.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2% PEG 400, 2M K2HPO4/NaH2PO4, 3mM farnesyl thiopyrophosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Oct 18, 2010 / Details: VariMaxHF
RadiationMonochromator: VariMaxHF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. all: 98794 / Num. obs: 97910 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Biso Wilson estimate: 49.7 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 23
Reflection shellResolution: 2.35→2.45 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 3.6 / Num. unique all: 9803 / % possible all: 98.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VJB

3vjb


Resolution: 2.35→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.913 / SU B: 18.685 / SU ML: 0.2 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25697 4876 5 %RANDOM
Rwork0.19035 ---
obs0.19364 97681 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.082 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å2-0.15 Å2
2--0.49 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15961 0 192 352 16505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02216471
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.96422271
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.21351963
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.26524.147803
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.717152921
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.83615112
X-RAY DIFFRACTIONr_chiral_restr0.0990.22462
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112412
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.5491.59847
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.902215956
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.45736624
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.784.56315
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.804316471
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.347→2.473 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.329 714 -
Rwork0.239 13094 -
obs-13808 96.42 %
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)
1-0.03940.05680.09090.24320.0845-0.0689-0.022-0.0295-0.0370.05560.01120.00630.05230.00670.01090.1028-0.00980.02390.0865-0.00360.15411.712859.259249.4836
20.0111-0.00810.01360.02260.00490.0158-0.0004-0.00080.00390.00610.0020.00340.00310.0021-0.00160.1246-0.00090.02810.1124-0.00090.167951.418844.119145.2793
3-0.15750.0926-0.02020.13020.0274-0.0634-0.01290.0040.06180.00430.0273-0.078-0.05550.0423-0.01440.0830.01930.01540.07320.01580.139718.423216.945843.2646
40.23110.0703-0.337-0.0089-0.15770.66340.0706-0.07060.05650.0848-0.017-0.015-0.15750.0477-0.05360.1789-0.02770.04210.1393-0.0070.213627.591768.0304-2.2264
50.06980.0108-0.01590.1251-0.05930.02920.00210.00720.009-0.00660.00260.00990.0037-0.0043-0.00470.12350.00120.02860.1124-0.00070.175-8.369948.46510.0786
60.27340.2166-0.03220.1064-0.06160.1336-0.01150.0239-0.0877-0.0556-0.0221-0.12640.04810.0360.03350.16960.01330.04920.14760.01060.217825.598824.3638-1.9186
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 369
2X-RAY DIFFRACTION1A401 - 402
3X-RAY DIFFRACTION2B37 - 369
4X-RAY DIFFRACTION2B401 - 402
5X-RAY DIFFRACTION3C36 - 368
6X-RAY DIFFRACTION3C401
7X-RAY DIFFRACTION4D37 - 369
8X-RAY DIFFRACTION4D401
9X-RAY DIFFRACTION5E37 - 369
10X-RAY DIFFRACTION5E401 - 402
11X-RAY DIFFRACTION6F38 - 369

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