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- PDB-3vjb: Crystal structure of the human squalene synthase -

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Basic information

Entry
Database: PDB / ID: 3vjb
TitleCrystal structure of the human squalene synthase
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsLiu, C.I. / Jeng, W.Y. / Chang, W.J. / Wang, A.H.J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Binding modes of zaragozic acid A to human squalene synthase and staphylococcal dehydrosqualene synthase
Authors: Liu, C.I. / Jeng, W.Y. / Chang, W.J. / Ko, T.P. / Wang, A.H.J.
History
DepositionOct 14, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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


Theoretical massNumber of molelcules
Total (without water)236,6946
Polymers236,6946
Non-polymers00
Water16,682926
1
A: Squalene synthase
B: Squalene synthase
C: Squalene synthase


Theoretical massNumber of molelcules
Total (without water)118,3473
Polymers118,3473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-30 kcal/mol
Surface area39340 Å2
MethodPISA
2
D: Squalene synthase
E: Squalene synthase
F: Squalene synthase


Theoretical massNumber of molelcules
Total (without water)118,3473
Polymers118,3473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-33 kcal/mol
Surface area39130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.610, 153.860, 91.516
Angle α, β, γ (deg.)90.00, 91.68, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 926 / 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: 2.55 Å3/Da / Density % sol: 51.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4M sodium citrate tribasic dihydrate, 0.1M HEPES sodium, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 19, 2007
Details: Vertically Collimating Premirror, Toroidal Focusing Mirror
RadiationMonochromator: LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. all: 147063 / Num. obs: 144874 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Biso Wilson estimate: 41.8 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 20.8
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 3.6 / Num. unique all: 14667 / % possible all: 91.4

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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: PDB ENTRY 1EZF

1ezf


Resolution: 2.05→29.4 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.941 / SU B: 10.58 / SU ML: 0.128 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22729 7255 5 %RANDOM
Rwork0.16874 ---
obs0.17164 144832 98.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.303 Å2
Baniso -1Baniso -2Baniso -3
1--2.6 Å20 Å22.49 Å2
2---1.49 Å20 Å2
3---4.24 Å2
Refinement stepCycle: LAST / Resolution: 2.05→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15962 0 0 926 16888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02216287
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.95222024
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4151962
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.4724.179804
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.502152919
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.69815111
X-RAY DIFFRACTIONr_chiral_restr0.1020.22448
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112291
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_it1.1831.59848
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.015215958
X-RAY DIFFRACTIONr_scbond_it3.33536439
X-RAY DIFFRACTIONr_scangle_it5.0784.56066
X-RAY DIFFRACTIONr_rigid_bond_restr1.759316287
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.052→2.162 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.258 967 -
Rwork0.198 18416 -
obs-19383 90.75 %
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)
11.06560.34780.01961.99490.39530.4580.0436-0.0790.0690.1933-0.0322-0.051-0.0044-0.0226-0.01140.05930.0088-0.01520.0159-0.00670.010910.998659.361549.3381
21.689-0.8315-0.22070.91970.02820.1431-0.0522-0.1535-0.08840.08950.0592-0.03630.00570.0524-0.0070.01080.0025-0.00650.08230.01080.075951.014944.004444.8275
32.08020.8548-0.51331.481-0.05720.32860.0865-0.2757-0.31750.1709-0.1431-0.32820.02730.0680.05660.0511-0.0148-0.0570.03740.04780.099917.444116.899742.6643
42.2517-0.4401-1.72670.856-0.08472.54960.3629-0.15970.29560.0644-0.0993-0.0321-0.52680.3436-0.26360.254-0.18060.05040.1969-0.040.044327.868867.5267-2.2683
51.71640.6773-0.20271.9608-0.05010.7632-0.12730.36970.1074-0.40870.11940.2724-0.141-0.11940.00790.21980.0262-0.08530.25840.02210.0454-8.399448.065910.0777
63.82050.7441-0.96841.6263-0.17991.2682-0.23420.5313-0.9267-0.5523-0.1552-0.39940.34920.10220.38940.30530.12330.18940.2985-0.06440.286725.744124.3183-1.3088
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 369
2X-RAY DIFFRACTION1A451 - 1376
3X-RAY DIFFRACTION2B37 - 369
4X-RAY DIFFRACTION2B452 - 1370
5X-RAY DIFFRACTION3C33 - 369
6X-RAY DIFFRACTION3C453 - 1371
7X-RAY DIFFRACTION4D37 - 369
8X-RAY DIFFRACTION4D474 - 1357
9X-RAY DIFFRACTION5E37 - 369
10X-RAY DIFFRACTION5E471 - 1375
11X-RAY DIFFRACTION6F37 - 369
12X-RAY DIFFRACTION6F586 - 1309

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