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Yorodumi- PDB-1wgc: 2.2 ANGSTROMS RESOLUTION STRUCTURE ANALYSIS OF TWO REFINED N-ACET... -
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-Basic information
Entry | Database: PDB / ID: 1wgc | ||||||||||||
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Title | 2.2 ANGSTROMS RESOLUTION STRUCTURE ANALYSIS OF TWO REFINED N-ACETYLNEURAMINYLLACTOSE-WHEAT GERM AGGLUTININ ISOLECTIN COMPLEXES | ||||||||||||
Components | WHEAT GERM LECTIN | ||||||||||||
Keywords | LECTIN (AGGLUTININ) | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Triticum aestivum (bread wheat) | ||||||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||||||||
Authors | Wright, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wgc.cif.gz | 76 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wgc.ent.gz | 60.1 KB | Display | PDB format |
PDBx/mmJSON format | 1wgc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wgc_validation.pdf.gz | 552.8 KB | Display | wwPDB validaton report |
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Full document | 1wgc_full_validation.pdf.gz | 568 KB | Display | |
Data in XML | 1wgc_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 1wgc_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/1wgc ftp://data.pdbj.org/pub/pdb/validation_reports/wg/1wgc | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given / Matrix: (1),Details | THE 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. | |
-Components
#1: Protein | Mass: 17124.080 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Triticum aestivum (bread wheat) / References: UniProt: P10968 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Water | ChemComp-HOH / | Compound details | ALPHA-HELIX AND BETA-SHEET ARE VIRTUALLY ABSENT IN THE STRUCTURAL | Nonpolymer details | N-ACETYLNNEURAMINYLLACTOSE IS NEUNAC-ALPHA(2-3)-GAL-BETA(1-4)-GLC. IN THIS ENTRY IT PRESENTED ON ...N-ACETYLNNEU | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.43 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 37 ℃ / pH: 4.9 / Method: unknown / Details: pH was adjusted to 4.9 with NaOH | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 8 Å / Num. obs: 17266 / % possible obs: 63 % / Observed criterion σ(I): 1 / Num. measured all: 10893 / Rmerge(I) obs: 0.082 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.2→8 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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Refinement | *PLUS σ(F): 1 / Highest resolution: 2.2 Å / Lowest resolution: 8 Å / Num. reflection obs: 10522 / Rfactor obs: 0.172 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 16.44 Å2 |