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Open data
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Basic information
Entry | Database: PDB / ID: 3enr | ||||||
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Title | ZINC-CALCIUM CONCANAVALIN A AT PH 6.15 | ||||||
![]() | Concanavalin-A | ||||||
![]() | CONCANAVALIN A / LECTIN / METAL BINDING / PH | ||||||
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. / Wyns, L. | ||||||
![]() | ![]() Title: Zinc/calcium- and cadmium/cadmium-substituted concanavalin A: interplay of metal binding, pH and molecular packing. Authors: Bouckaert, J. / Loris, R. / Wyns, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.2 KB | Display | ![]() |
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PDB format | ![]() | 80.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.4 KB | Display | ![]() |
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Full document | ![]() | 435.2 KB | Display | |
Data in XML | ![]() | 20.3 KB | Display | |
Data in CIF | ![]() | 27.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2enrC ![]() 5cnaS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.973159, 0.23012, -0.002408), Vector: Details | THE ASSYMMETRIC UNIT CONTAINS A DIMER. THE BIOLOGICALLY ACTIVE UNIT IS A CANONICAL DIMER OR A TETRAMER (ABOVE PH 6.5). THE FOLLOWING SURFACE LOOPS ARE IN WEAK ELECTRON DENSITY: 118-123 AND 160-163. A ZN2+ IS SUBSTITUTED FOR MN2+ IN THE TRANSITION METAL ION SITE S1. THE CALCIUM SITE S2 CONTAINS CA2+. | |
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Components
#1: Protein | Mass: 25622.385 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ZINC/CALCIUM COMPLEX / Source: (natural) ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 41.3 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6.15 Details: ZNCL2, CACL2, (NH4)2SO4, sodium acetate, pH 6.15, VAPOR DIFFUSION, SITTING DROP | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 6, 1996 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→15 Å / Num. all: 20384 / Num. obs: 20384 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 49.4 Å2 / Rsym value: 0.103 / Net I/σ(I): 16.38 |
Reflection shell | Resolution: 2.4→2.48 Å / Redundancy: 6 % / Mean I/σ(I) obs: 7.34 / Rsym value: 0.29 / % possible all: 99.1 |
Reflection | *PLUS Num. measured all: 132328 / Rmerge(I) obs: 0.103 |
Reflection shell | *PLUS % possible obs: 99.1 % / Rmerge(I) obs: 0.29 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: DIMER OF PDB ENTRY 5CNA Resolution: 2.4→15 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 45.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→15 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.51 Å / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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