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

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Basic information

Entry
Database: PDB / ID: 3vjc
TitleCrystal structure of the human squalene synthase in complex with zaragozic acid A
ComponentsSqualene synthase
KeywordsTransferase/Transferase inhibitor / Farnesyl-diphosphate farnesyltransferase / Head-to-head synthases / Cholesterol biosynthesis / Oxidoreductase / Transferase-Transferase inhibitor complex
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
PHOSPHATE ION / Zaragozic acid A / Squalene synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsLiu, C.I. / Jeng, W.Y. / Chang, W.J. / Ko, T.P. / 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 ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 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)241,45720
Polymers236,6946
Non-polymers4,76314
Water25,0411390
1
A: Squalene synthase
B: Squalene synthase
C: Squalene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,72810
Polymers118,3473
Non-polymers2,3817
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-53 kcal/mol
Surface area39020 Å2
MethodPISA
2
D: Squalene synthase
E: Squalene synthase
F: Squalene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,72810
Polymers118,3473
Non-polymers2,3817
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-51 kcal/mol
Surface area38930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.873, 153.153, 91.855
Angle α, β, γ (deg.)90.00, 91.72, 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-ZGA / Zaragozic acid A / (1S,3S,4S,5R,6R,7R)-1-[(4S,5R)-4-(acetyloxy)-5-methyl-3-methylidene-6-phenylhexyl]-6-{[(2E,4S,6S)-4,6-dimethyloct-2-eno yl]oxy}-4,7-dihydroxy-2,8-dioxabicyclo[3.2.1]octane-3,4,5-tricarboxylic acid


Mass: 690.731 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C35H46O14
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1390 / 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: 51.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2% PEG 400, 2M K2HPO4/NaH2PO4, 0.5mM zaragozic acid A, pH 6.5, 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 315r / Detector: CCD / Date: Jul 24, 2009
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: 1.89→30 Å / Num. all: 189042 / Num. obs: 187887 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 31.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.8
Reflection shellResolution: 1.89→1.96 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 2.3 / Num. unique all: 18909 / % possible all: 99.2

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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: 1.89→27.7 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.16 / SU ML: 0.082 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19717 9431 5 %RANDOM
Rwork0.14787 ---
obs0.15035 187819 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.25 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å20 Å21.36 Å2
2---0.39 Å20 Å2
3---1.72 Å2
Refinement stepCycle: LAST / Resolution: 1.89→27.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16139 0 326 1390 17855
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02216799
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.41.97422761
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.88451991
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.25124.141809
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.552152963
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.10915114
X-RAY DIFFRACTIONr_chiral_restr0.0950.22532
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112616
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_it1.2461.59967
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.083216150
X-RAY DIFFRACTIONr_scbond_it3.34536832
X-RAY DIFFRACTIONr_scangle_it5.0264.56611
X-RAY DIFFRACTIONr_rigid_bond_restr1.723316799
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.89→1.992 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.255 1376 -
Rwork0.183 25845 -
obs-27221 99 %
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)
10.72690.2467-0.03191.19180.14210.38240.0197-0.05030.04980.097-0.00620.0202-0.0122-0.0242-0.01360.0450.0092-0.01320.0075-0.0060.010611.338258.658449.643
21.1147-0.3662-0.31810.72350.0860.259-0.0088-0.1088-0.01780.02240.0248-0.0880.00540.0714-0.0160.0039-0.0023-0.00910.03980.0110.031651.068143.84344.7978
31.19760.3835-0.08820.4488-0.03190.30250.0175-0.0689-0.17220.0226-0.0395-0.08380.06910.01910.02210.0519-0.0023-0.02170.00730.02120.078417.590816.617442.6951
41.52130.0365-1.30930.5413-0.51791.67540.2201-0.18330.19230.00170.01910.0507-0.23450.2563-0.23920.1416-0.12730.05020.1779-0.0610.038728.465967.0415-2.2757
51.41540.4985-0.40171.055-0.45930.8764-0.06490.46550.1203-0.06250.21290.1536-0.0571-0.2274-0.14810.0404-0.0185-0.01260.23220.07950.0464-8.265848.59710.1224
62.23410.9617-1.15811.5134-0.45451.0247-0.08920.1598-0.5151-0.2424-0.2564-0.36380.21210.01490.34560.11470.08820.08690.2059-0.00610.169824.559924.5279-2.0274
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 369
2X-RAY DIFFRACTION1A400 - 401
3X-RAY DIFFRACTION1A451 - 1836
4X-RAY DIFFRACTION2B37 - 369
5X-RAY DIFFRACTION2B400 - 402
6X-RAY DIFFRACTION2B465 - 1834
7X-RAY DIFFRACTION3C37 - 368
8X-RAY DIFFRACTION3C400 - 401
9X-RAY DIFFRACTION3C592 - 1837
10X-RAY DIFFRACTION4D37 - 369
11X-RAY DIFFRACTION4D400 - 402
12X-RAY DIFFRACTION4D504 - 1838
13X-RAY DIFFRACTION5E37 - 369
14X-RAY DIFFRACTION5E400 - 401
15X-RAY DIFFRACTION5E569 - 1839
16X-RAY DIFFRACTION6F38 - 369
17X-RAY DIFFRACTION6F400 - 401
18X-RAY DIFFRACTION6F857 - 1840

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