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- PDB-2uvo: High Resolution Crystal Structure of Wheat Germ Agglutinin in Com... -

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Basic information

Entry
Database: PDB / ID: 2uvo
TitleHigh Resolution Crystal Structure of Wheat Germ Agglutinin in Complex with N-Acetyl-D-Glucosamine
ComponentsAGGLUTININ ISOLECTIN 1
KeywordsCARBOHYDRATE-BINDING PROTEIN / HEVEIN DOMAIN / CHITIN-BINDING / WHEAT GERM AGGLUTININ / CHITIN-BINDING PROTEIN / N-ACETYL-D- GLUCOSAMINE / WGA / GLCNAC / CHITIN / LECTIN / ANTIFUNGAL / PROTEIN-CARBOHYDRATE INTERACTION
Function / homology
Function and homology information


chitin binding / catalytic activity / carbohydrate binding
Similarity search - Function
Endochitinase-like / Chitin-binding, type 1, conserved site / Chitin recognition protein / Chitin recognition or binding domain signature. / Chitin-binding type-1 domain profile. / Chitin binding domain / Chitin-binding, type 1 / Endochitinase-like superfamily / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-glucopyranose / Agglutinin isolectin 1
Similarity search - Component
Biological speciesTRITICUM AESTIVUM (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSchwefel, D. / Wittmann, V. / Diederichs, K. / Welte, W.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: Structural Basis of Multivalent Binding to Wheat Germ Agglutinin.
Authors: Schwefel, D. / Maierhofer, C. / Beck, J.G. / Seeberger, S. / Diederichs, K. / Moller, H.M. / Welte, W. / Wittmann, V.
History
DepositionMar 13, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 11, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Polymer sequence
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity_poly / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can ..._chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_validate_symm_contact / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_validate_symm_contact.auth_atom_id_2
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 3.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AGGLUTININ ISOLECTIN 1
B: AGGLUTININ ISOLECTIN 1
E: AGGLUTININ ISOLECTIN 1
F: AGGLUTININ ISOLECTIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,84626
Polymers68,4964
Non-polymers4,35022
Water11,223623
1
A: AGGLUTININ ISOLECTIN 1
B: AGGLUTININ ISOLECTIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,64414
Polymers34,2482
Non-polymers2,39612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-36 kcal/mol
Surface area17940 Å2
MethodPQS
2
E: AGGLUTININ ISOLECTIN 1
F: AGGLUTININ ISOLECTIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,20212
Polymers34,2482
Non-polymers1,95410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-41.1 kcal/mol
Surface area18040 Å2
MethodPQS
Unit cell
Length a, b, c (Å)44.390, 91.510, 94.500
Angle α, β, γ (deg.)90.00, 82.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
AGGLUTININ ISOLECTIN 1 / WGA1 / ISOLECTIN A / WHEAT GERM AGGLUTININ


Mass: 17124.080 Da / Num. of mol.: 4 / Fragment: RESIDUES 27-197 / Source method: isolated from a natural source / Source: (natural) TRITICUM AESTIVUM (bread wheat) / References: UniProt: P10968
#2: Sugar
ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: 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.: 9
Source method: isolated from a genetically manipulated source
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
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 623 / Source method: isolated from a natural source / Formula: H2O
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: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growDetails: CRYSTALLIZATION BUFFER: 20 MM SODIUM ACETATE, 6 MM CACL2, 4 % ETHANOL RESERVOIR: 0.04 M POTASSIUM DIHYDROGEN PHOSPHATE, 16 % PEG 8000, 20 % GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→37.48 Å / Num. obs: 137253 / % possible obs: 93.5 % / Observed criterion σ(I): 2 / Redundancy: 3.75 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.87
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3.77 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.27 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.3.0022refinement
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WGT

1wgt


Resolution: 1.4→93.66 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.223 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FOLLOWING RESIDUES WERE MODELED IN ATERNATIVE CONFORMATIONS LYS A 33, LYS A 134, SER A 152, MET B 26, MET E 10, LEU E 16, LYS E 33, ALA E ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FOLLOWING RESIDUES WERE MODELED IN ATERNATIVE CONFORMATIONS LYS A 33, LYS A 134, SER A 152, MET B 26, MET E 10, LEU E 16, LYS E 33, ALA E 53, MET F 10, MET F 26, SER F 91, ARG F 139. FOLLOWING RESIDUES WERE MODELED WITH OCCUPANCY LOWER THAN 1 BECAUSE OF RADIATION DAMAGE OR MISSING DENSITY DUE TO FLEXIBILITY GLU A 5, GLU B 5, GLU E 5, GLY E 171, GLU F 5, ASP F 135, GLY F 171.
RfactorNum. reflection% reflectionSelection details
Rfree0.204 6879 5 %RANDOM
Rwork0.181 ---
obs0.182 130373 93.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.12 Å2
2--0.41 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.4→93.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4663 0 294 623 5580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0215190
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.17527012
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4085707
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.0625.337193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.00115704
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.7831517
X-RAY DIFFRACTIONr_chiral_restr0.0830.2672
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023977
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.270.22496
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.23612
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.10.2559
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.299
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.250
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9261.53397
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.26125121
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.34432051
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6544.51878
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.29 511
Rwork0.278 9907

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