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- PDB-2x3t: Glutaraldehyde-crosslinked wheat germ agglutinin isolectin 1 crys... -

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Basic information

Entry
Database: PDB / ID: 2x3t
TitleGlutaraldehyde-crosslinked wheat germ agglutinin isolectin 1 crystal soaked with a synthetic glycopeptide
Components
  • AGGLUTININ ISOLECTIN 1
  • GLYCOPEPTIDE
KeywordsSUGAR BINDING PROTEIN/PEPTIDE / SUGAR BINDING PROTEIN-PEPTIDE COMPLEX / CHITIN-BINDING
Function / homology
Function and homology information


chitin binding / 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
D-ALPHA-AMINOBUTYRIC ACID / Chem-GYV / Agglutinin isolectin 1
Similarity search - Component
Biological speciesTRITICUM AESTIVUM (bread wheat)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.749 Å
AuthorsSchwefel, D. / Maierhofer, C. / 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
DepositionJan 26, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Refinement description / Version format compliance
Revision 1.2Dec 28, 2016Group: Source and taxonomy
Revision 2.0Mar 11, 2020Group: Derived calculations / Other / Polymer sequence / Category: entity_poly / pdbx_database_status / struct_conn
Item: _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: Atomic model / Data collection ...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 / 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 / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 4.0Aug 5, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_entity_nonpoly
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 / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 4.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 5.0May 1, 2024Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can

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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
C: AGGLUTININ ISOLECTIN 1
D: AGGLUTININ ISOLECTIN 1
E: GLYCOPEPTIDE
M: GLYCOPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,17327
Polymers70,2686
Non-polymers3,90521
Water68538
1
C: AGGLUTININ ISOLECTIN 1
D: AGGLUTININ ISOLECTIN 1
M: GLYCOPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,85712
Polymers35,1343
Non-polymers1,7239
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-38.8 kcal/mol
Surface area17880 Å2
MethodPQS
2
A: AGGLUTININ ISOLECTIN 1
B: AGGLUTININ ISOLECTIN 1
E: GLYCOPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,31615
Polymers35,1343
Non-polymers2,18212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7770 Å2
ΔGint-33.6 kcal/mol
Surface area17660 Å2
MethodPQS
Unit cell
Length a, b, c (Å)44.640, 93.210, 92.500
Angle α, β, γ (deg.)90.00, 98.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide / Sugars , 3 types, 17 molecules ABCDEM

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


Mass: 17124.080 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TRITICUM AESTIVUM (bread wheat) / References: UniProt: P10968
#2: Protein/peptide GLYCOPEPTIDE


Mass: 886.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Sugar
ChemComp-GYV / 2-acetamido-1-O-carbamoyl-2-deoxy-alpha-D-glucopyranose / 2-(ACETYLAMINO)-1-O-CARBAMOYL-2-DEOXY-ALPHA-D-GLUCOPYRANOSE / 2-acetamido-1-O-carbamoyl-2-deoxy-alpha-D-glucose / 2-acetamido-1-O-carbamoyl-2-deoxy-D-glucose / 2-acetamido-1-O-carbamoyl-2-deoxy-glucose


Type: D-saccharide / Mass: 264.233 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Formula: C9H16N2O7
IdentifierTypeProgram
methyl-a-D-glucopyranosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 48 molecules

#4: Chemical
ChemComp-DBB / D-ALPHA-AMINOBUTYRIC ACID


Type: D-peptide linking / Mass: 103.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H9NO2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsGYV, DBB (RESIDUES 1170-1173 CHAINS A, B, C, D): CANNOT BE ASSIGNED SEPARATE CHAIN IDS FOR THE ...GYV, DBB (RESIDUES 1170-1173 CHAINS A, B, C, D): CANNOT BE ASSIGNED SEPARATE CHAIN IDS FOR THE CYCLIC LIGAND. IN ABSENCE OF BACKBONE DENSITY, IT IS NOT POSSIBLE TO IDENTIFY THEIR SPECIFIC POSITIONS IN THE CYCLIC LIGAND SINCE THEY MIGHT BE ANY OF THE THREE EQUIVALENT DBB-GYV ADDUCTS.

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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: 2.83 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 4.9
Details: 0.04M KH2PO4, 20% GLYCEROL, 14%-17% PEG 8000, pH 4.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 19531 / % possible obs: 99.5 % / Observed criterion σ(I): 3.45 / Redundancy: 3.8 % / Biso Wilson estimate: 42.32 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.1
Reflection shellResolution: 2.75→2.91 Å / Redundancy: 3.78 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.45 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 7WGA

7wga


Resolution: 2.749→32.653 Å / SU ML: 0.46 / σ(F): 1.99 / Phase error: 33.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2847 1000 5.1 %
Rwork0.2285 --
obs0.2315 19531 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.65 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso mean: 55.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.7783 Å20 Å20.146 Å2
2--17.1332 Å20 Å2
3----16.3548 Å2
Refinement stepCycle: LAST / Resolution: 2.749→32.653 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4545 0 237 38 4820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024929
X-RAY DIFFRACTIONf_angle_d0.7216528
X-RAY DIFFRACTIONf_dihedral_angle_d22.3651746
X-RAY DIFFRACTIONf_chiral_restr0.038599
X-RAY DIFFRACTIONf_plane_restr0.006898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7493-2.89410.39411340.32592618X-RAY DIFFRACTION99
2.8941-3.07530.37521410.28852634X-RAY DIFFRACTION100
3.0753-3.31260.34021460.27392649X-RAY DIFFRACTION100
3.3126-3.64550.29521530.22722627X-RAY DIFFRACTION100
3.6455-4.17210.23041440.18872664X-RAY DIFFRACTION100
4.1721-5.25290.24511430.1762651X-RAY DIFFRACTION100
5.2529-32.65540.26181390.22852688X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 5.0362 Å / Origin y: 22.9398 Å / Origin z: 22.8769 Å
111213212223313233
T0.253 Å20.0284 Å2-0.03 Å2-0.5414 Å2-0.0523 Å2--0.2409 Å2
L0.0279 °20.1068 °20.1219 °2-0.062 °20.0743 °2--0.1178 °2
S-0.0792 Å °-0.226 Å °0.0122 Å °-0.0107 Å °0.0272 Å °0.1124 Å °-0.0299 Å °-0.2107 Å °0.0219 Å °
Refinement TLS groupSelection details: ALL

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