+Open data
-Basic information
Entry | Database: PDB / ID: 1c3k | ||||||
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Title | CRYSTAL STRUCTURE OF HELIANTHUS TUBEROSUS LECTIN | ||||||
Components | AGGLUTININ | ||||||
Keywords | SUGAR BINDING PROTEIN / BETA PRISM / AGGLUTININ / JACALIN-RELATED / MANNOSE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Helianthus tuberosus (Jerusalem artichoke) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Bourne, Y. / Zamboni, V. / Barre, A. / Peumans, W.J. / van Damme, E.J.M. / Rouge, P. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 1999 Title: Helianthus tuberosus lectin reveals a widespread scaffold for mannose-binding lectins. Authors: Bourne, Y. / Zamboni, V. / Barre, A. / Peumans, W.J. / Van Damme, E.J. / Rouge, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c3k.cif.gz | 40.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c3k.ent.gz | 28.6 KB | Display | PDB format |
PDBx/mmJSON format | 1c3k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/1c3k ftp://data.pdbj.org/pub/pdb/validation_reports/c3/1c3k | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15501.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TUBER Source: (natural) Helianthus tuberosus (Jerusalem artichoke) References: UniProt: Q9ZQY5 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.52 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7 Details: 26-28% PEG MONOMETHYL ESTER 550, 0.2 M MAGNESIUM ACETATE, pH 7.0, VAPOR DIFFUSION, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.835 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 11, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.835 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 11028 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.233 / % possible all: 91.2 |
Reflection | *PLUS Num. measured all: 86459 |
Reflection shell | *PLUS % possible obs: 92.3 % / Mean I/σ(I) obs: 3.1 |
-Processing
Software |
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Refinement | Resolution: 2→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2→15 Å
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Refine LS restraints |
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Software | *PLUS Name: 'CNS' / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 11024 / % reflection Rfree: 5 % / Rfactor all: 0.199 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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