+Open data
-Basic information
Entry | Database: PDB / ID: 1jly | ||||||
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Title | CRYSTAL STRUCTURE OF AMARANTHUS CAUDATUS AGGLUTININ | ||||||
Components | AGGLUTININ | ||||||
Keywords | LECTIN / AGGLUTININ / T-DISACCHARIDE HOMODIMER / BIVALENT | ||||||
Function / homology | 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 / Agglutinin Function and homology information | ||||||
Biological species | Amaranthus caudatus (amaranth) | ||||||
Method | X-RAY DIFFRACTION / MIR / 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 | 1jly.cif.gz | 133.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jly.ent.gz | 109.8 KB | Display | PDB format |
PDBx/mmJSON format | 1jly.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jl/1jly ftp://data.pdbj.org/pub/pdb/validation_reports/jl/1jly | 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.839, -0.544), Vector: |
-Components
#1: Protein | Mass: 34824.332 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Amaranthus caudatus (amaranth) / Organ: SEED / References: UniProt: Q71QF2 #2: 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: 1 |
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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: 296 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: ADSC / Detector: AREA DETECTOR / Date: Mar 1, 1994 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 36419 / % possible obs: 92.3 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.3 |
Reflection shell | Highest resolution: 2.2 Å / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 2.6 / % possible all: 72.2 |
Reflection | *PLUS Highest resolution: 2.2 Å |
Reflection shell | *PLUS % possible obs: 72.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / 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: 18.6 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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