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- PDB-6xrx: Crystal structure of the mosquito protein AZ1 as an MBP fusion -

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Basic information

Entry
Database: PDB / ID: 6xrx
TitleCrystal structure of the mosquito protein AZ1 as an MBP fusion
ComponentsMaltose/maltodextrin-binding periplasmic protein, Mosquito protein AZ1
KeywordsLIPID BINDING PROTEIN / mosquito / fatty acids / lipids / anti-viral
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
Insect allergen-related / Insect allergen related repeat, nitrile-specifier detoxification / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / AAEL010431-PA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Aedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPedersen, L.C. / Mueller, G.A. / Foo, A.C.Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIA- ES102645 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01- ES102906 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: The mosquito protein AEG12 displays both cytolytic and antiviral properties via a common lipid transfer mechanism.
Authors: Foo, A.C.Y. / Thompson, P.M. / Chen, S.H. / Jadi, R. / Lupo, B. / DeRose, E.F. / Arora, S. / Placentra, V.C. / Premkumar, L. / Perera, L. / Pedersen, L.C. / Martin, N. / Mueller, G.A.
History
DepositionJul 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein, Mosquito protein AZ1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8507
Polymers61,3291
Non-polymers5216
Water9,908550
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.013, 113.013, 83.442
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Space group name HallP62
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Maltose/maltodextrin-binding periplasmic protein, Mosquito protein AZ1


Mass: 61329.234 Da / Num. of mol.: 1 / Mutation: surface entropy reduction mutations in MBP
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Aedes aegypti (yellow fever mosquito)
Strain: K12 / Gene: malE, b4034, JW3994, AAEL010431, AAEL013577 / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / References: UniProt: P0AEX9, UniProt: Q8T5C5
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 555 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Sequence detailsIn this construct, mosquito protein AZ1 is the C-terminal domain of this MBP fusion protein

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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: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 20% PEG 1000, 50mM MES, 100mM NaCl, 200mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 44356 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 17.51 Å2 / Rpim(I) all: 0.022 / Rrim(I) all: 0.056 / Rsym value: 0.051 / Net I/σ(I): 10.9
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2.26 / Num. unique obs: 2211 / CC1/2: 0.742 / CC star: 0.923 / Rpim(I) all: 0.337 / Rrim(I) all: 0.861 / Rsym value: 0.792 / Χ2: 0.882 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T05, 4JRB

5t05

4jrb


Resolution: 1.95→33.82 Å / SU ML: 0.1712 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 19.3604
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2012 2221 5.02 %
Rwork0.1765 41995 -
obs0.1778 44216 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.24 Å2
Refinement stepCycle: LAST / Resolution: 1.95→33.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4223 0 31 550 4804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00324417
X-RAY DIFFRACTIONf_angle_d0.58136027
X-RAY DIFFRACTIONf_chiral_restr0.0405670
X-RAY DIFFRACTIONf_plane_restr0.0033785
X-RAY DIFFRACTIONf_dihedral_angle_d15.72071542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.990.23481350.21852540X-RAY DIFFRACTION96.5
1.99-2.040.21421360.20852586X-RAY DIFFRACTION99.45
2.04-2.090.25081350.20242625X-RAY DIFFRACTION100
2.09-2.140.2361420.1952612X-RAY DIFFRACTION100
2.14-2.210.22131360.18422601X-RAY DIFFRACTION100
2.21-2.280.19171420.17862618X-RAY DIFFRACTION100
2.28-2.360.2271390.17652654X-RAY DIFFRACTION100
2.36-2.450.23141360.17452626X-RAY DIFFRACTION100
2.45-2.570.23131400.1822626X-RAY DIFFRACTION100
2.57-2.70.22281430.17412640X-RAY DIFFRACTION100
2.7-2.870.19891310.18072625X-RAY DIFFRACTION100
2.87-3.090.20471370.1832625X-RAY DIFFRACTION100
3.09-3.40.2031390.16922626X-RAY DIFFRACTION100
3.4-3.890.16721440.15692652X-RAY DIFFRACTION100
3.89-4.90.17281400.15592668X-RAY DIFFRACTION100
4.9-33.820.17921460.17972671X-RAY DIFFRACTION99.51
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)
12.240663245340.100179763401-0.2357936722521.719544444830.06868688702261.640185047570.0704568097649-0.265429428004-0.06506639159590.219103381787-0.0301148712626-0.0292450702358-0.122197184729-0.0334751242544-0.01843591107840.105235790538-0.00411709685967-0.01449869680310.1331543031290.0111205886750.018440901451943.667479937590.08347771334.26784229064
21.39463430120.674082555677-0.3222092261671.01610661252-0.2317587300030.653134915239-0.008929726129560.0429977478991-0.154156179538-0.05269642106870.03459013131940.1275055149270.105225401585-0.0722599555468-0.02904290701830.09877040310340.00157694722059-0.02832779970740.07374247300720.02258664954170.099409270039825.426083023280.5051273401-3.03247848777
39.03210902918-2.65852066146-2.18063079799.39215679306-1.422015814792.511614731140.244992813981.58467644210.587875611448-1.49302250160.1253524354690.33132093954-0.548642847727-0.304342114916-0.3853277442690.393678711623-0.0267940360747-0.02722023387340.3436526160980.1527712361640.37263080669812.123095612293.3551326167-9.4097391462
41.631114289731.02322406368-0.4156085793071.50180148347-0.3476749648030.6598802475440.0618056960922-0.0860263065866-0.2092133875030.0637816267789-0.04702278923210.07294084063530.138385155493-0.0941702493646-0.018328857590.117389706178-0.0194133058607-0.02949191736850.1012516017630.02072383663970.12443932724722.768433408275.08336831271.67437235824
52.253271747061.088570353910.1905177795881.47903999540.1700977185591.6325269367-0.08164964067390.217880540704-0.267084192015-0.267635065520.0855500142155-0.07404390100270.189751366740.0208067246069-0.01993585918250.126370396565-1.27731221589E-7-0.004218229734960.097662274086-0.01898748706360.065789771012239.648076841881.5783975631-10.871374532
61.59688605022-0.216379230206-0.235222164841.457715234580.09677562312410.810536205340.0939963003447-0.1270687479230.2102380449890.301720895417-0.01762703228790.327335123002-0.104810381376-0.208030095928-0.02570828976280.212650625669-0.002101515290710.06836038428970.135594752033-0.004461997162680.1964370058912.535755754390.14898921967.70669734904
70.391613617996-1.40320434044-0.820257223645.073149747383.279141280644.33979684248-0.2826648788880.591188277646-0.5206585065120.218680703617-0.4569211163580.5559835946850.277303558758-0.8995181291550.5505728863420.1801459108830.03066455578580.03709564985850.38158445598-0.2025549496360.423676347120.559252579371119.6784579229.5347178295
80.9541487260140.501332305498-0.2405353758860.55059715863-0.6821182538891.141672491180.0771986269016-0.03917730466110.239256644863-0.327722416278-0.01212260037-0.275032197484-0.386663213467-0.0719534978405-0.260652549520.3899707018440.146894402613-0.008562294350740.172385240596-0.1361265735090.4037384033439.32878755715132.42582398226.6110479229
91.7261289753-0.2133519848641.192603640485.735874903931.182390872493.69793725889-0.009915347776430.04797618630610.261292429204-0.2015923780590.190124281079-0.140034046176-0.2025448215870.45990631947-0.1331941824610.263786988329-0.061675331920.1010883447550.160217396979-0.07156294718360.28311620640111.7749346064122.1764244310.0623933612
100.913410748552-0.765504051085-0.1895514131011.079672196781.251565387052.67776829413-0.224700228489-0.1437988343370.2843916092660.2345586203610.495047185462-0.4347753151180.2851367714720.794641492248-0.1793753646690.2767279364910.0746817223258-0.01787169101740.378504665814-0.1419559583080.4599060683116.6589635804116.95973187722.7566474028
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:55)
2X-RAY DIFFRACTION2(chain A and resid 56:168)
3X-RAY DIFFRACTION3(chain A and resid 169:175)
4X-RAY DIFFRACTION4(chain A and resid 176:273)
5X-RAY DIFFRACTION5(chain A and resid 274:322)
6X-RAY DIFFRACTION6(chain A and resid 323:1037)
7X-RAY DIFFRACTION7(chain A and resid 1038:1051)
8X-RAY DIFFRACTION8(chain A and resid 1052:1066)
9X-RAY DIFFRACTION9(chain A and resid 1067:1107)
10X-RAY DIFFRACTION10(chain A and resid 1108:1204)

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