+Open data
-Basic information
Entry | Database: PDB / ID: 1jlx | |||||||||
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Title | AGGLUTININ IN COMPLEX WITH T-DISACCHARIDE | |||||||||
Components | AGGLUTININ | |||||||||
Keywords | LECTIN / COMPLEX (LECTIN-SACCHARIDE) / T-DISACCHARIDE HOMODIMER / BIVALENT | |||||||||
Function / homology | Function and homology information Agglutinin domain / Agglutinin domain superfamily / Agglutinin domain / Agglutinin / : / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta Similarity search - Domain/homology | |||||||||
Biological species | Amaranthus caudatus (amaranth) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Transue, T.R. / Smith, A.K. / Mo, H. / Goldstein, I.J. / Saper, M.A. | |||||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1997 Title: Structure of benzyl T-antigen disaccharide bound to Amaranthus caudatus agglutinin. Authors: Transue, T.R. / Smith, A.K. / Mo, H. / Goldstein, I.J. / Saper, M.A. #1: Journal: J.Biol.Chem. / Year: 1989 Title: Isolation and Characterization of Amaranthin, a Lectin Present in the Seeds of Amaranthus Caudatus, that Recognizes the T-(or Cryptic T)-Antigen Authors: Rinderle, S.J. / Goldstein, I.J. / Matta, K.L. / Ratcliffe, R.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jlx.cif.gz | 135.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jlx.ent.gz | 109.9 KB | Display | PDB format |
PDBx/mmJSON format | 1jlx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jlx_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1jlx_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1jlx_validation.xml.gz | 26.6 KB | Display | |
Data in CIF | 1jlx_validation.cif.gz | 37.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jl/1jlx ftp://data.pdbj.org/pub/pdb/validation_reports/jl/1jlx | HTTPS FTP |
-Related structure data
Related structure data | 1jlySC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 34812.324 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Amaranthus caudatus (amaranth) / Organ: SEED / References: PIR: S24263, UniProt: Q71QF2*PLUS #2: Polysaccharide | #3: Chemical | ChemComp-FOR / #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE WAS DEDUCED FROM THE KNOWN SEQUENCE OF AN APPARENT HOMOLOGUE FROM AMARANTHUS ...THE SEQUENCE WAS DEDUCED FROM THE KNOWN SEQUENCE OF AN APPARENT HOMOLOGUE FROM AMARANTHUS | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 57 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.7 / Details: pH 6.7 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908 |
Detector | Detector: CCD / Date: Aug 7, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.908 Å / Relative weight: 1 |
Reflection | Num. obs: 33071 / % possible obs: 88.4 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 11.3 |
Reflection shell | Highest resolution: 2.2 Å / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 7.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JLY Resolution: 2.2→10 Å / σ(F): 0 Details: THE N-TERMINAL ALA 1 APPEARS TO HAVE DENSITY CONSISTENT WITH A FORMYL GROUP ATTACHED TO THE N-TERMINUS.
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Displacement parameters | Biso mean: 23.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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