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- PDB-9g3q: Chitinase-like protein AgBR1 from Aedes aegypti -

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Basic information

Entry
Database: PDB / ID: 9g3q
TitleChitinase-like protein AgBR1 from Aedes aegypti
ComponentsAAEL001965-PA
KeywordsUNKNOWN FUNCTION / GH18 family chitinase-like protein / Aedes aegypti salivary gland protein
Function / homology
Function and homology information


chitinase activity / chitin catabolic process / chitin binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
Imaginal disc growth factor / : / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
D-MALATE / AAEL001965-PA
Similarity search - Component
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsAbrescia, N.G.A. / Martinez-Castillo, A.
Funding support Spain, 3items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)RTI2018-095700-B-I00 Spain
Agencia Estatal de Investigacion (AEI)PID2021-126130OB-I00 Spain
Department of Education of the Basque GovernmentPRE_2018_1_0102 Spain
Citation
Journal: J.Virol. / Year: 2025
Title: Structural and functional significance of Aedes aegypti AgBR1 flavivirus immunomodulator.
Authors: Martinez-Castillo, A. / Barriales, D. / Azkargorta, M. / Zalamea, J.D. / Arda, A. / Jimenez-Barbero, J. / Gonzalez-Lopez, M. / Aransay, A.M. / Marin-Lopez, A. / Fikrig, E. / Elortza, F. / ...Authors: Martinez-Castillo, A. / Barriales, D. / Azkargorta, M. / Zalamea, J.D. / Arda, A. / Jimenez-Barbero, J. / Gonzalez-Lopez, M. / Aransay, A.M. / Marin-Lopez, A. / Fikrig, E. / Elortza, F. / Anguita, J. / Abrescia, N.G.A.
#1: Journal: J.Biol.Chem. / Year: 2002
Title: Crystal structure of imaginal disc growth factor-2. A member of a new family of growth-promoting glycoproteins from Drosophila melanogaster.
Authors: Varela, P.F. / Llera, A.S. / Mariuzza, R.A. / Tormo, J.
#2: Journal: J.Biol.Chem. / Year: 2015
Title: Structural and thermodynamic insights into chitooligosaccharide binding to human cartilage chitinase 3-like protein 2 (CHI3L2 or YKL-39).
Authors: Ranok, A. / Wongsantichon, J. / Robinson, R.C. / Suginta, W.
History
DepositionJul 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 28, 2025Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jun 4, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AAEL001965-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3773
Polymers47,8191
Non-polymers5582
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint8 kcal/mol
Surface area17220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.432, 77.191, 51.116
Angle α, β, γ (deg.)90.000, 104.840, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein AAEL001965-PA


Mass: 47818.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Protein expressed in pOPIN G vector. The protein contains a signal peptide at the N-ter, that is cleaved leaving ETG extra residues. At the C-ter, the protein contains a His-tag (KHHHHHH). ...Details: Protein expressed in pOPIN G vector. The protein contains a signal peptide at the N-ter, that is cleaved leaving ETG extra residues. At the C-ter, the protein contains a His-tag (KHHHHHH). The protein crystal structure lacks a flexible loop from residues 166-185 (residue numbers corresponds to the model). The structure begins at residue Gly24 (residue number 7 in the alignment above).
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Strain: Ho Chi Minh / Gene: AAEL001965 / Plasmid: pOPIN G / Production host: Homo sapiens (human) / References: UniProt: Q17JL7
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O
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: 2.05 Å3/Da / Density % sol: 39.93 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 4
Details: Thawed AgBR1 protein was desalted with 150 mM NaCl, 50 mM Tris, pH 7.4 buffer using Micro Bio-Spin columns (Biorad) to eliminate glycerol. The measured nanodrop absorbance was 8.7 mg/mL. 75 ...Details: Thawed AgBR1 protein was desalted with 150 mM NaCl, 50 mM Tris, pH 7.4 buffer using Micro Bio-Spin columns (Biorad) to eliminate glycerol. The measured nanodrop absorbance was 8.7 mg/mL. 75 nL of protein were mixed with 150 nL of crystallization reservoir buffer contaning 0.1 M MMT, 25% PEG 1,500 from PACT Premier.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.2→49.41 Å / Num. obs: 81290 / % possible obs: 93.5 % / Redundancy: 6.68 % / Biso Wilson estimate: 14.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.018 / Rrim(I) all: 0.048 / Net I/σ(I): 15.9
Reflection shellResolution: 1.204→1.328 Å / Redundancy: 4.98 % / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 1.525 / Num. unique obs: 4065 / CC1/2: 0.7312 / Rpim(I) all: 0.355 / Rrim(I) all: 0.829 / % possible all: 51.34

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→49.41 Å / SU ML: 0.1192 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.3372
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1796 3991 4.91 %
Rwork0.1477 77295 -
obs0.1493 81286 69.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.1 Å2
Refinement stepCycle: LAST / Resolution: 1.2→49.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3145 0 37 332 3514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00983359
X-RAY DIFFRACTIONf_angle_d1.03924583
X-RAY DIFFRACTIONf_chiral_restr0.0873493
X-RAY DIFFRACTIONf_plane_restr0.0094607
X-RAY DIFFRACTIONf_dihedral_angle_d11.82231269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.220.310470.2674134X-RAY DIFFRACTION3.54
1.22-1.230.578750.2168160X-RAY DIFFRACTION4.21
1.23-1.250.205590.2259239X-RAY DIFFRACTION6.21
1.25-1.270.3227260.2416347X-RAY DIFFRACTION9.26
1.27-1.280.2861340.2147540X-RAY DIFFRACTION14.41
1.28-1.30.2781540.2103815X-RAY DIFFRACTION21.68
1.3-1.320.2218590.20751125X-RAY DIFFRACTION29.53
1.32-1.340.2711750.20841481X-RAY DIFFRACTION38.75
1.34-1.360.231220.20582045X-RAY DIFFRACTION53.95
1.36-1.390.23451140.20842291X-RAY DIFFRACTION60.79
1.39-1.410.23081290.19772590X-RAY DIFFRACTION67.07
1.41-1.440.23981280.1862790X-RAY DIFFRACTION72.59
1.44-1.470.21231420.17092943X-RAY DIFFRACTION77.32
1.47-1.50.22431820.17533120X-RAY DIFFRACTION82.06
1.5-1.540.2211420.16833335X-RAY DIFFRACTION87.16
1.54-1.570.20741620.15813520X-RAY DIFFRACTION91.46
1.57-1.620.21991800.16173772X-RAY DIFFRACTION98.38
1.62-1.660.1912070.16153810X-RAY DIFFRACTION99.98
1.66-1.720.19691950.15333838X-RAY DIFFRACTION99.88
1.72-1.780.1882060.14753787X-RAY DIFFRACTION99.95
1.78-1.850.17952060.14583823X-RAY DIFFRACTION99.98
1.85-1.930.19072010.1443855X-RAY DIFFRACTION100
1.93-2.040.17881710.13573836X-RAY DIFFRACTION100
2.04-2.160.16062170.13323803X-RAY DIFFRACTION100
2.16-2.330.17072180.13313829X-RAY DIFFRACTION99.98
2.33-2.570.15671770.13333869X-RAY DIFFRACTION99.98
2.57-2.940.1652020.14823830X-RAY DIFFRACTION100
2.94-3.70.17992270.14383850X-RAY DIFFRACTION100
3.7-49.410.16491940.14633918X-RAY DIFFRACTION99.93

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