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- PDB-7wgi: Crystal structure of AflSQS from Aspergillus flavus -

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Basic information

Entry
Database: PDB / ID: 7wgi
TitleCrystal structure of AflSQS from Aspergillus flavus
ComponentsSqualene synthase
KeywordsBIOSYNTHETIC PROTEIN / isoprenoid synthase
Function / homology
Function and homology information


squalene synthase / farnesyl-diphosphate farnesyltransferase activity / squalene synthase activity / sterol biosynthetic process / membrane => GO:0016020
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. / Squalene/phytoene synthase / Trans-isoprenyl diphosphate synthases, head-to-head / Squalene/phytoene synthase / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
INDOLE / PHOSPHATE ION / Squalene synthase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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)54,9633
Polymers54,7511
Non-polymers2122
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-6 kcal/mol
Surface area15530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.468, 206.468, 206.468
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number196
Space group name H-MF23

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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-IND / INDOLE


Mass: 117.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7N / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 3.35 Å3/Da / Density % sol: 63.27 %
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: Oct 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 25222 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.913 / Net I/σ(I): 31.05
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 2.18 / Num. unique obs: 2508 / CC1/2: 0.626 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EZF

1ezf


Resolution: 2.5→24.33 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.22 1274 5.05 %
Rwork0.195 23947 -
obs0.197 25221 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.72 Å2 / Biso mean: 63.68 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.5→24.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2864 0 14 76 2954
Biso mean--85.99 56.41 -
Num. residues----349
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5-2.60.31531420.28726472789
2.6-2.720.33351460.279726672813
2.72-2.860.31271350.252526432778
2.86-3.040.2881390.244826452784
3.04-3.280.28171420.242326302772
3.28-3.610.28851430.206826322775
3.61-4.120.18991410.176726592800
4.13-5.190.1921390.173726872826
5.19-24.330.15771470.156527372884

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