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- PDB-1ces: CRYSTALS OF DEMETALLIZED CONCANAVALIN A SOAKED WITH ZINC HAVE A Z... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ces | ||||||
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Title | CRYSTALS OF DEMETALLIZED CONCANAVALIN A SOAKED WITH ZINC HAVE A ZINC ION BOUND IN THE S1 SITE | ||||||
![]() | CONCANAVALIN A | ||||||
![]() | LECTIN / CONCANAVALIN A / ZINC / CONFORMATION | ||||||
Function / homology | ![]() regulation of defense response to virus / D-mannose binding / defense response / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Bouckaert, J. / Loris, R. / Poortmans, F. / Wyns, L. | ||||||
![]() | ![]() Title: Sequential structural changes upon zinc and calcium binding to metal-free concanavalin A. Authors: Bouckaert, J. / Poortmans, F. / Wyns, L. / Loris, R. #1: ![]() Title: Crystallographic Structure of Metal-Free Concanavalin a at 2.5 A Resolution Authors: Bouckaert, J. / Loris, R. / Poortmans, F. / Wyns, L. | ||||||
History |
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Remark 700 | SHEET THE MOST STRIKING FEATURE OF CONCANAVALIN A IS TWO LARGE BETA SHEETS IN THE STRUCTURE ...SHEET THE MOST STRIKING FEATURE OF CONCANAVALIN A IS TWO LARGE BETA SHEETS IN THE STRUCTURE COMPRISING 119 OF THE 237 AMINO ACIDS. THERE IS NO ALPHA HELIX. THE REMAINING AMINO ACIDS FORM A SERIES OF LOOPS AND TURNS. CONCANAVALIN A EXISTS AS A TETRAMER ALTHOUGH THE ASYMMETRIC UNIT CONTAINS A DIMER. THE TETRAMER CAN BE GENERATED BY SYMMETRY OPERATORS. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.6 KB | Display | ![]() |
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PDB format | ![]() | 74.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1enqC ![]() 1enrC ![]() 1ensC ![]() 1apnS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25622.385 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THERE ARE TWO MONOMERS (MR 25500 EACH) WITH IDENTICAL SEQUENCE Source: (natural) ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | ZINC ION IS PARTIALLY BOUND IN THE S1 SITE. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 45.9 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 / Details: pH 5. | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ![]() |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jun 9, 1993 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→10 Å / Num. obs: 12557 / % possible obs: 91.5 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.085 |
Reflection | *PLUS Num. measured all: 29303 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: DEMETALLIZED CONCANAVALIN A (PDB ENTRY 1APN) Resolution: 2.7→10 Å / Cross valid method: BRUNGER / σ(F): 0
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Displacement parameters | Biso mean: 24.89 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→10 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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