1B2P | pdb_00001b2p

NATIVE MANNOSE-SPECIFIC BULB LECTIN FROM SCILLA CAMPANULATA (BLUEBELL) AT 1.7 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.208 (Depositor) 
  • R-Value Work: 
    0.186 (Depositor), 0.163 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Structure of the native (unligated) mannose-specific bulb lectin from Scilla campanulata (bluebell) at 1.7 A resolution.

Wood, S.D.Wright, L.M.Reynolds, C.D.Rizkallah, P.J.Allen, A.K.Peumans, W.J.Van Damme, E.J.

(1999) Acta Crystallogr D Biol Crystallogr 55: 1264-1272

  • DOI: https://doi.org/10.1107/s0907444999005326
  • Primary Citation Related Structures: 
    1B2P

  • PubMed Abstract: 

    The X-ray crystal structure of native Scilla campanulata agglutinin, a mannose-specific lectin from bluebell bulbs and a member of the Liliaceae family, has been determined by molecular replacement and refined to an R value of 0.186 at 1.7 A resolution. The lectin crystallizes in space group P21212 with unit-cell parameters a = 70. 42, b = 92.95, c = 46.64 A. The unit cell contains eight protein molecules of Mr = 13143 Da (119 amino-acid residues). The asymmetric unit comprises two chemically identical molecules, A and B, related by a non-crystallographic twofold axis perpendicular to c. This dimer further associates by crystallographic twofold symmetry to form a tetramer. The fold of the polypeptide backbone closely resembles that found in the lectins from Galanthus nivalis (snowdrop) and Hippeastrum (amaryllis) and contains a threefold symmetric beta-prism made up of three antiparallel four-stranded beta-sheets. Each of the four-stranded beta-sheets (I, II and III) possesses a potential saccharide-binding site containing conserved residues; however, site II has two mutations relative to sites I and III which may prevent ligation at this site. Our study provides the first accurate and detailed description of a native (unligated) structure from this superfamily of mannose-specific bulb lectins and will allow comparisons with a number of lectin-saccharide complexes which have already been determined or are currently under investigation.


  • Organizational Affiliation
    • School of Biomolecular Sciences, Max Perutz Building, Liverpool John Moores University, Liverpool L3 3AF, England.

Macromolecule Content 

  • Total Structure Weight: 26.42 kDa 
  • Atom Count: 2,109 
  • Modeled Residue Count: 238 
  • Deposited Residue Count: 238 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTEIN (LECTIN)
A, B
119Hyacinthoides hispanicaMutation(s): 0 
UniProt
Find proteins for Q9ZP49 (Hyacinthoides hispanica)
Explore Q9ZP49 
Go to UniProtKB:  Q9ZP49
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZP49
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.208 (Depositor) 
  • R-Value Work:  0.186 (Depositor), 0.163 (DCC) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.42α = 90
b = 92.95β = 90
c = 46.64γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
ROTAVATAdata reduction
AMoREphasing
REFMACrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-07-22
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-08-09
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary