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- PDB-3aqx: Crystal structure of Bombyx mori beta-GRP/GNBP3 N-terminal domain... -

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Basic information

Entry
Database: PDB / ID: 3aqx
TitleCrystal structure of Bombyx mori beta-GRP/GNBP3 N-terminal domain with laminarihexaoses
ComponentsBeta-1,3-glucan-binding protein
KeywordsSUGAR BINDING PROTEIN / beta-sandwich / Immune receptor / beta-1 / 3-glucan
Function / homology
Function and homology information


polysaccharide immune receptor activity / (1->3)-beta-D-glucan binding / cell surface pattern recognition receptor signaling pathway / regulation of innate immune response / pattern recognition receptor activity / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / innate immune response / extracellular region
Similarity search - Function
Beta-1,3-glucan-recognition protein, N-terminal domain / Beta-1,3-glucan-binding protein, N-terminal / Beta-1,3-glucan recognition protein, C-terminal / Beta-1,3-glucan-binding protein, N-terminal domain superfamily / Carbohydrate binding domain (family 32) / CBM39 (carbohydrate binding type-39) domain profile. / : / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. ...Beta-1,3-glucan-recognition protein, N-terminal domain / Beta-1,3-glucan-binding protein, N-terminal / Beta-1,3-glucan recognition protein, C-terminal / Beta-1,3-glucan-binding protein, N-terminal domain superfamily / Carbohydrate binding domain (family 32) / CBM39 (carbohydrate binding type-39) domain profile. / : / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Beta-1,3-glucan-binding protein
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsKanagawa, M. / Satoh, T. / Ikeda, A. / Adachi, Y. / Ohno, N. / Yamaguchi, Y.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural insights into recognition of triple-helical beta-glucans by an insect fungal receptor
Authors: Kanagawa, M. / Satoh, T. / Ikeda, A. / Adachi, Y. / Ohno, N. / Yamaguchi, Y.
History
DepositionNov 22, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references / Derived calculations
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Beta-1,3-glucan-binding protein
B: Beta-1,3-glucan-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7045
Polymers23,6302
Non-polymers2,0743
Water3,765209
1
A: Beta-1,3-glucan-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8062
Polymers11,8151
Non-polymers9911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-1,3-glucan-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8983
Polymers11,8151
Non-polymers1,0832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.210, 74.210, 47.603
Angle α, β, γ (deg.)90, 90, 90
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Beta-1,3-glucan-binding protein / BGBP / Beta-1 / 3-glucan recognition protein / BetaGRP


Mass: 11815.192 Da / Num. of mol.: 2 / Fragment: beta-glucan binding domain, UNP residues 17-118
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Plasmid: pCold-I(MBP-TRX fusion) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: Q9NL89
#2: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D- ...beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 990.860 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1b_1-5]/1-1-1-1-1-1/a3-b1_b3-c1_c3-d1_d3-e1_e3-f1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

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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: 2.77 Å3/Da / Density % sol: 55.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M ammonium sulfate, 0.1M HEPES sodium buffer, 10% (w/v) PEG 4000, 5mM laminarihexaose, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 6, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 16433 / Num. obs: 16156 / % possible obs: 98.3 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.172 / Net I/σ(I): 9.1
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 2 / Num. unique all: 692 / % possible all: 87.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IE4

3ie4


Resolution: 2.05→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.086 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.216 812 5 %RANDOM
Rwork0.174 ---
obs0.177 15273 98.09 %-
all-15273 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.777 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1630 0 140 209 1979
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211973
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5122.12704
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2485199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.33323.33387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.12515271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0661512
X-RAY DIFFRACTIONr_chiral_restr0.0970.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211322
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7791.5991
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.43821582
X-RAY DIFFRACTIONr_scbond_it2.1283982
X-RAY DIFFRACTIONr_scangle_it3.314.51122
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 46 -
Rwork0.228 994 -
obs--88.44 %

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