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- PDB-8slv: Structure of a salivary alpha-glucosidase from the mosquito vecto... -

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Basic information

Entry
Database: PDB / ID: 8slv
TitleStructure of a salivary alpha-glucosidase from the mosquito vector Aedes aegypti.
ComponentsSalivary alpha-glucosidase
KeywordsHYDROLASE / Salivary alpha-glucosidase / mosquito
Function / homology
Function and homology information


: / alpha-glucosidase
Similarity search - Function
Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
CYSTEINE / ISOPROPYL ALCOHOL / 1,3-PROPANDIOL / Probable maltase
Similarity search - Component
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsGittis, A.G. / Williams, A.E. / Garboczi, D. / Calvo, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Insect Biochem.Mol.Biol. / Year: 2024
Title: Structural and functional comparisons of salivary alpha-glucosidases from the mosquito vectors Aedes aegypti, Anopheles gambiae, and Culex quinquefasciatus.
Authors: Williams, A.E. / Gittis, A.G. / Botello, K. / Cruz, P. / Martin-Martin, I. / Valenzuela Leon, P.C. / Sumner, B. / Bonilla, B. / Calvo, E.
History
DepositionApr 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Salivary alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,04417
Polymers66,7611
Non-polymers1,28316
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Dynamic Light Scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.760, 51.030, 70.750
Angle α, β, γ (deg.)101.816, 94.658, 95.764
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Salivary alpha-glucosidase


Mass: 66760.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Gene: MAL1, MAL I, AAEL000392 / Production host: Homo sapiens (human) / References: UniProt: P13080, alpha-glucosidase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 8 types, 342 molecules

#3: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#7: Chemical ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#9: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 51.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.2 M magnesium chloride hexahydrate, , 0.1 M HEPES sodium pH 7.5, 30% v/v 2-propanol

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Data collection

DiffractionMean temperature: 95.5 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: DECTRIS EIGER2 R 4M / Detector: PIXEL / Date: Jul 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.32→24.79 Å / Num. obs: 27047 / % possible obs: 94.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 19.86 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.039 / Net I/σ(I): 26.95
Reflection shellResolution: 2.32→2.38 Å / Redundancy: 2.88 % / Mean I/σ(I) obs: 11.82 / Num. unique obs: 1623 / CC1/2: 0.98 / Rrim(I) all: 0.106 / % possible all: 78.4

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→22.55 Å / SU ML: 0.2075 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 18.5432
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1884 1998 7.39 %
Rwork0.1459 25030 -
obs0.149 27028 94.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.48 Å2
Refinement stepCycle: LAST / Resolution: 2.32→22.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4505 0 74 327 4906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01134691
X-RAY DIFFRACTIONf_angle_d1.20756374
X-RAY DIFFRACTIONf_chiral_restr0.0732670
X-RAY DIFFRACTIONf_plane_restr0.0067826
X-RAY DIFFRACTIONf_dihedral_angle_d17.73131693
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.380.20711140.1461421X-RAY DIFFRACTION77.1
2.38-2.440.20641430.15411797X-RAY DIFFRACTION93.81
2.44-2.510.23831400.1521761X-RAY DIFFRACTION94.39
2.51-2.60.22531420.15751793X-RAY DIFFRACTION95.41
2.6-2.690.22181460.1631822X-RAY DIFFRACTION95.53
2.69-2.80.22881430.1591798X-RAY DIFFRACTION95.62
2.8-2.920.22131440.16561797X-RAY DIFFRACTION95.99
2.92-3.080.20151470.16841831X-RAY DIFFRACTION96.25
3.08-3.270.21111450.15221826X-RAY DIFFRACTION96.81
3.27-3.520.18921460.151827X-RAY DIFFRACTION96.91
3.52-3.870.1481460.13531830X-RAY DIFFRACTION97.44
3.87-4.430.14641490.12021867X-RAY DIFFRACTION97.77
4.43-5.570.16941480.12511851X-RAY DIFFRACTION98.52
5.57-22.550.1731450.15071809X-RAY DIFFRACTION96.11

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