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Yorodumi- PDB-1scs: HIGH-RESOLUTION STRUCTURES OF SINGLE-METAL-SUBSTITUTED CONCANAVAL... -
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-Basic information
Entry | Database: PDB / ID: 1scs | ||||||
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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 | ||||||
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: 1.6 Å | ||||||
Authors | Emmerich, C. / Helliwell, J.R. / Redshaw, M. / Naismith, J.H. / Harrop, S.J. / Raftery, J. / Kalb, A.J. / Yariv, J. / Dauter, Z. / Wilson, K.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1994 Title: High-resolution structures of single-metal-substituted concanavalin A: the Co,Ca-protein at 1.6 A and the Ni,Ca-protein at 2.0 A. Authors: Emmerich, C. / Helliwell, J.R. / Redshaw, M. / Naismith, J.H. / Harrop, S.J. / Raftery, J. / Kalb, A.J. / Yariv, J. / Dauter, Z. / Wilson, K.S. #1: Journal: Embo J. / Year: 1992 Title: Non-Glycosylated Recombinant Pro-Concanavalin a is Active without Polypeptide Cleavage Authors: Min, W. / Dunn, A.J. / Jones #2: Journal: Acta Crystallogr.,Sect.D / Year: 1993 Title: The Refined Structure of Cadmium Substituted Concanavalin a at 2.0 Angstroms Resolution Authors: Naismith, J.H. / Habash, J. / Harrop, S.J. / Helliwell, J.R. / Hunter, W.N. / Wan, T.C.M. / Weisgerber, S. / Kalb(Gilboa), A.J. / Yariv, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1scs.cif.gz | 60.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1scs.ent.gz | 44.4 KB | Display | PDB format |
PDBx/mmJSON format | 1scs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sc/1scs ftp://data.pdbj.org/pub/pdb/validation_reports/sc/1scs | HTTPS FTP |
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-Related structure data
-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 207 - ASP 208 OMEGA = 5.01 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION | ||||||||
Components on special symmetry positions |
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Details | THERE IS ONE MONOMER (237 AMINO ACIDS) IN THE ASYMMETRIC UNIT. CONCANAVALIN A EXISTS AS A TETRAMER ALTHOUGH THE ASYMMETRIC UNIT CONTAINS A MONOMER. THE TETRAMER CAN BE GENERATED BY SYMMETRY OPERATORS. |
-Components
#1: Protein | Mass: 25622.385 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Canavalia ensiformis (jack bean) / Gene: CDNA / Organ: BEAN / References: UniProt: P02866 |
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#2: Chemical | ChemComp-CO / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE IS AS DERIVED FROM THE CDNA SEQUENCE OF MIN ET AL.,1992. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.4 % |
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Crystal grow | *PLUS Method: other / Details: Kalb, A.J., (1988) J. Crystal Growth, 88, 537. |
-Data collection
Reflection | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 8 Å / Num. obs: 30245 / % possible obs: 91.9 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.048 |
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-Processing
Software |
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Refinement | Resolution: 1.6→8 Å / σ(F): 1 /
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Refinement step | Cycle: LAST / Resolution: 1.6→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.178 / Rfactor Rwork: 0.178 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.8 |