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- PDB-9wga: 2.2 ANGSTROMS RESOLUTION STRUCTURE ANALYSIS OF TWO REFINED N-ACET... -

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Entry
Database: PDB / ID: 9wga
Title2.2 ANGSTROMS RESOLUTION STRUCTURE ANALYSIS OF TWO REFINED N-ACETYLNEURAMINYLLACTOSE-WHEAT GERM AGGLUTININ ISOLECTIN COMPLEXES
ComponentsWHEAT GERM LECTIN
KeywordsLECTIN (AGGLUTININ)
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
Agglutinin isolectin 2
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsWright, C.S.
Citation
Journal: J.Mol.Biol. / Year: 1990
Title: 2.2 A resolution structure analysis of two refined N-acetylneuraminyl-lactose--wheat germ agglutinin isolectin complexes.
Authors: Wright, C.S.
#1: Journal: J.Mol.Biol. / Year: 1989
Title: Comparison of the Refined Crystal Structures of Two Wheat Germ Isolectins
Authors: Wright, C.S.
#2: Journal: J.Mol.Evol. / Year: 1989
Title: Sequence Variability in Three Wheat Germ Agglutinin Isolectins. Products of Multiple Genes in Polyploid Wheat
Authors: Wright, C.S. / Raikhel, N.
#3: Journal: J.Mol.Biol. / Year: 1988
Title: Erratum. Refinement of the Crystal Structure of Wheat Germ Agglutinin Isolectin 2 at 1.8 Angstroms Resolution
Authors: Wright, C.S.
#4: Journal: J.Mol.Biol. / Year: 1987
Title: Refinement of the Crystal Structure of Wheat Germ Agglutinin Isolectin 2 at 1.8 Angstroms Resolution
Authors: Wright, C.S.
#5: Journal: J.Mol.Biol. / Year: 1987
Title: Preliminary X-Ray Diffraction Results on Co-Crystals of Wheat Germ Agglutinin with a Sialoglycopeptide from the Red Cell Receptor Glycophorina
Authors: Wright, C.S. / Kahane, I.
#6: Journal: J.Biol.Chem. / Year: 1986
Title: Structural Differences in the Two Major Wheat Germ Agglutinin Isolectins
Authors: Wright, C.S. / Olafsdottir, S.
#7: Journal: J.Mol.Evol. / Year: 1985
Title: Evolution of the Multidomain Protein Wheat Germ Agglutinin
Authors: Wright, H.T. / Brooks, D.M. / Wright, C.S.
#8: Journal: J.Mol.Biol. / Year: 1984
Title: Structural Comparison of the Two Distinct Sugar Binding Sites in Wheat Germ Agglutinin Isolectin II
Authors: Wright, C.S.
#9: Journal: Biochemistry / Year: 1984
Title: Primary Structure of Wheat Germ Agglutinin Isolectin 2. Peptide Order Deduced from X-Ray Structure
Authors: Wright, C.S. / Gavilanes, F. / Peterson, D.L.
#10: Journal: J.Mol.Biol. / Year: 1981
Title: Histidine Determination in Wheat Germ Agglutinin Isolectin by X-Ray Diffraction Analysis
Authors: Wright, C.S.
#11: Journal: Biomolecular Structure, Conformation, Function and Evolution
Year: 1980
Title: Multi-Domain Structure of the Dimeric Lectin Wheat Germ Agglutinin
Authors: Wright, C.S.
#12: Journal: J.Mol.Biol. / Year: 1980
Title: Location of the N-Acetyl-D-Neuraminic Acid Binding Site in Wheat Germ Agglutinin. A Crystallographic Study at 2.8 Angstroms Resolution
Authors: Wright, C.S.
#13: Journal: J.Biol.Chem. / Year: 1980
Title: The Toxin-Agglutinin Fold. A New Group of Small Protein Structures Organized Around a Four-Disulfide Core
Authors: Drenth, J. / Low, B.W. / Richardson, J.S. / Wright, C.S.
#14: Journal: J.Mol.Biol. / Year: 1980
Title: Crystallographic Elucidation of the Saccharide Binding Mode in Wheat Germ Agglutinin and its Biological Significance
Authors: Wright, C.S.
#15: Journal: J.Mol.Biol. / Year: 1977
Title: The Crystal Structure of Wheat Germ Agglutinin at 2.2 Angstroms Resolution
Authors: Wright, C.S.
#16: Journal: J.Mol.Biol. / Year: 1974
Title: Non-Crystallographic Symmetry in the Crystal Dimer of Wheat Germ Agglutinin
Authors: Wright, C.S.
#17: Journal: J.Mol.Biol. / Year: 1974
Title: A Preliminary Crystallographic Study of Wheat Germ Agglutinin
Authors: Wright, C.S. / Keith, C. / Langridge, R. / Nagata, Y. / Burger, M.M.
History
DepositionApr 20, 1990Processing site: BNL
SupersessionOct 15, 1990ID: 3WGA
Revision 1.0Oct 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WHEAT GERM LECTIN
B: WHEAT GERM LECTIN


Theoretical massNumber of molelcules
Total (without water)34,2702
Polymers34,2702
Non-polymers00
Water4,161231
1
A: WHEAT GERM LECTIN

A: WHEAT GERM LECTIN


Theoretical massNumber of molelcules
Total (without water)34,2702
Polymers34,2702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4600 Å2
ΔGint-27 kcal/mol
Surface area14550 Å2
MethodPISA, PQS
2
B: WHEAT GERM LECTIN


Theoretical massNumber of molelcules
Total (without water)17,1351
Polymers17,1351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: WHEAT GERM LECTIN

B: WHEAT GERM LECTIN


Theoretical massNumber of molelcules
Total (without water)34,2702
Polymers34,2702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)51.340, 73.530, 91.540
Angle α, β, γ (deg.)90.00, 97.59, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-210-

HOH

21A-223-

HOH

31A-247-

HOH

41A-253-

HOH

51B-190-

HOH

61B-212-

HOH

71B-263-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (1), (-1), (-1) / Vector: -6.04, -0.0738, 45.36)
DetailsTHE TRANSFORMATION GIVEN ON THE *MTRIX* RECORDS BELOW YIELDS COORDINATES FOR PROTOMER II WHEN APPLIED TO PROTOMER I. IT REPRESENTS THE NON-CRYSTALLOGRAPHIC SCREW DIAD AXIS RELATING PROTOMERS OF ADJACENT DIMERS.

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Components

#1: Protein WHEAT GERM LECTIN


Mass: 17135.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum aestivum (bread wheat) / References: UniProt: P02876
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Compound detailsALPHA-HELIX AND BETA-SHEET ARE VIRTUALLY ABSENT IN THE STRUCTURAL DOMAIN OF WGA.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal grow
*PLUS
Temperature: 37 ℃ / pH: 4.9 / Method: unknown / Details: pH was adjusted to 4.9 with NaOH
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16-8 mg/mlprotein1drop
23-5 %ethanol1reservoir
36 mM1reservoirCaCl2

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→8 Å / σ(F): 3 /
RfactorNum. reflection
obs0.175 17318
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2313 0 0 231 2544
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.040.035
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0370.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.12
X-RAY DIFFRACTIONp_mcangle_it3.173
X-RAY DIFFRACTIONp_scbond_it2.272
X-RAY DIFFRACTIONp_scangle_it3.53
X-RAY DIFFRACTIONp_plane_restr0.0180.025
X-RAY DIFFRACTIONp_chiral_restr0.2160.2
X-RAY DIFFRACTIONp_singtor_nbd0.1990.5
X-RAY DIFFRACTIONp_multtor_nbd0.2020.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2450.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.83
X-RAY DIFFRACTIONp_staggered_tor21.315
X-RAY DIFFRACTIONp_orthonormal_tor42.720
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 8 Å / Num. reflection obs: 17318 / σ(F): 3 / Rfactor obs: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS

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