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- PDB-7wgh: Crystal structure of AflSQS from Aspergillus flavus in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7wgh
TitleCrystal structure of AflSQS from Aspergillus flavus in complex with FSPP
ComponentsSqualene synthase
KeywordsBIOSYNTHETIC PROTEIN / isoprenoid synthase
Function / homology
Function and homology information


squalene synthase / farnesyl diphosphate metabolic process / squalene synthase [NAD(P)H] activity / D-glucose transmembrane transporter activity / ergosterol biosynthetic process / endoplasmic reticulum 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 / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
Chem-FPS / PHOSPHATE ION / PYROPHOSPHATE 2- / Squalene synthase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsShang, N. / Liu, W.D. / Chen, C.C. / Guo, R.T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Omega / Year: 2022
Title: A Structural and Bioinformatics Investigation of a Fungal Squalene Synthase and Comparisons with Other Membrane Proteins.
Authors: Malwal, S.R. / Shang, N. / Liu, W. / Li, X. / Zhang, L. / Chen, C.C. / Guo, R.T. / Oldfield, E.
History
DepositionDec 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Squalene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9956
Polymers54,7511
Non-polymers1,2445
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-6 kcal/mol
Surface area15750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.339, 208.339, 208.339
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-660-

HOH

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Components

#1: Protein Squalene synthase


Mass: 54750.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus flavus (mold)
Gene: BDV35DRAFT_364291, CA14_004282, F9C07_2287043, G4B11_012149
Plasmid: pET46 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A364LX79, squalene synthase
#2: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: 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.: 2 / Source method: obtained synthetically / Formula: C15H28O6P2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.44 Å3/Da / Density % sol: 64.25 % / Mosaicity: 0.435 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.1 M NaH2PO4, 0.5 M K2HPO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.9998 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 27, 2019
RadiationMonochromator: LN2 cooled Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.36→25 Å / Num. obs: 30779 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 49.88 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 15
Reflection shellResolution: 2.36→2.44 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.834 / Num. unique obs: 3031 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EZF

1ezf


Resolution: 2.36→24.55 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 1545 5.02 %
Rwork0.188 29231 -
obs0.189 30776 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.7 Å2 / Biso mean: 55.33 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.36→24.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2871 0 52 104 3027
Biso mean--79.86 56.16 -
Num. residues----350
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.36-2.440.28891530.251928853038
2.45-2.540.28731570.243329253082
2.54-2.660.28251560.236528933049
2.66-2.80.28391540.220229003054
2.8-2.970.28661510.219629093060
2.97-3.20.25741510.227929443095
3.2-3.520.23861540.195528923046
3.53-4.030.22051580.173129193077
4.03-5.070.16111560.165129603116
5.08-24.550.19321550.161130043159

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