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Yorodumi- PDB-5cna: REFINED STRUCTURE OF CONCANAVALIN A COMPLEXED WITH ALPHA-METHYL-D... -
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-Basic information
Entry | Database: PDB / ID: 5cna | |||||||||
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Title | REFINED STRUCTURE OF CONCANAVALIN A COMPLEXED WITH ALPHA-METHYL-D-MANNOPYRANOSIDE AT 2.0 ANGSTROMS RESOLUTION AND COMPARISON WITH THE SACCHARIDE-FREE STRUCTURE | |||||||||
Components | CONCANAVALIN A | |||||||||
Keywords | LECTIN(AGGLUTININ) | |||||||||
Function / homology | Function and homology information regulation of defense response to virus / D-mannose binding / defense response / metal ion binding Similarity search - Function | |||||||||
Biological species | Canavalia ensiformis (jack bean) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | |||||||||
Authors | Naismith, J.H. / Emmerich, C. / Habash, J. / Harrop, S.J. / Helliwell, J.R. / Hunter, W.N. / Raftery, J. / Kalb(Gilboa), A.J. / Yariv, J. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1994 Title: Refined structure of concanavalin A complexed with methyl alpha-D-mannopyranoside at 2.0 A resolution and comparison with the saccharide-free structure. Authors: Naismith, J.H. / Emmerich, C. / Habash, J. / Harrop, S.J. / Helliwell, J.R. / Hunter, W.N. / Raftery, J. / Kalb, A.J. / Yariv, J. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1994 Title: High-Resolution Structures of Single-Metal-Substituted Concanavalin A: The Co,Ca-Protein at 1.6 Angstroms and the Ni,Ca-Protein at 2.0 Angstroms Authors: Emmerich, C. / Helliwell, J.R. / Redshaw, M. / Naismith, J.H. / Harrop, S.J. / Raftery, J. / Kalb(Gilboa), A.J. / Yariv, J. / Dauter, Z. / Wilson, K.S. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1993 Title: Refined Structure of Cadmium-Substituted Concanavalin a at 2.0 Angstroms Resolution Authors: Naismith, J.H. / Habash, J. / Harrop, S. / Helliwell, J.R. / Hunter, W.N. / Wan, T.C.M. / Weisgerber, S. / Kalb(Gilboa), A.J. / Yariv, J. #3: Journal: J.Chem.Soc.,Faraday Trans. / Year: 1993 Title: High-Resolution Crystallographic Studies of Native Concanavalin a Using Rapid Laue Data Collection Methods and the Introduction of a Monochromatic Large-Angle Oscillation Technique (Lot) Authors: Weisgerber, S. / Helliwell, J.R. #4: Journal: Embo J. / Year: 1992 Title: Non-Glycosylated Recombinant Pro-Concanavalin a is Active without Polypeptide Cleavage Authors: Min, W. / Dunn, A.J. / Jones #5: Journal: Embo J. / Year: 1989 Title: The Structure of the Saccharide Binding-Site of Concanavalin A Authors: Derewenda, Z. / Yariv, J. / Helliwell, J.R. / Kalb(Gilboa), A.J. / Dodson, E.J. / Papiz, M.Z. / Wan, T. / Campbell, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cna.cif.gz | 204.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cna.ent.gz | 164 KB | Display | PDB format |
PDBx/mmJSON format | 5cna.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/5cna ftp://data.pdbj.org/pub/pdb/validation_reports/cn/5cna | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: ALA A 207 - ASP A 208 OMEGA = 0.18 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: ALA B 207 - ASP B 208 OMEGA =359.31 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 3: ALA C 207 - ASP C 208 OMEGA = 0.18 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 4: ALA D 207 - ASP D 208 OMEGA = 1.05 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 5: THE ATOMS LABELLED OD1 AND OD2 IN ASP 10 OF EACH SUBUNIT HAVE BEEN INTERCHANGED COMPARED WITH THE LABELS IN THE PUBLISHED PAPERS. |
-Components
-Protein / Sugars , 2 types, 8 molecules ABCD
#1: Protein | Mass: 25622.385 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Canavalia ensiformis (jack bean) / Gene: CDNA / Organ: BEAN / References: UniProt: P02866 #2: Sugar | ChemComp-MMA / |
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-Non-polymers , 4 types, 542 molecules
#3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE SEQUENCE HAS NOT BEEN REPORTED. IT WAS DERIVED FROM THE CDNA SEQUENCE OF MIN ET AL., 1992, ...THE SEQUENCE HAS NOT BEEN REPORTED. IT WAS DERIVED FROM THE CDNA SEQUENCE OF MIN ET AL., 1992, LISTED AS REFERENCE 3 ABOVE. |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.81 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.8 / Method: microdialysis | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 8 Å / Num. obs: 58871 / % possible obs: 82 % / Observed criterion σ(F): 1 / Num. measured all: 62198 / Rmerge(I) obs: 0.076 |
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-Processing
Software |
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Refinement | Resolution: 2→8 Å / σ(F): 1 Details: THE THREE RAMACHANDRAN OUTLIERS THR A 120, HIS A 121 AND SER B 204) DESCRIBED IN NAISMITH ET AL. ARE IN POORLY DEFINED REGIONS OF ELECTRON DENSITY.
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.199 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 32 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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