7ELV | pdb_00007elv

Structure of legume lectin domain from Methanocaldococcus jannaschii in apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.175 (Depositor), 0.176 (DCC) 
  • R-Value Work: 
    0.154 (Depositor), 0.154 (DCC) 
  • R-Value Observed: 
    0.155 (Depositor) 

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

Crystal structure of an L-type lectin domain from archaea.

Khan, F.Kaza, S.

(2023) Proteins 91: 456-465

  • DOI: https://doi.org/10.1002/prot.26440
  • Primary Citation Related Structures: 
    7ELV, 7EXO

  • PubMed Abstract: 

    The crystal structures of an L-type lectin domain from Methanocaldococcus jannaschii in apo and mannose-bound forms have been determined. A thorough investigation of L-type lectin domains from several organisms provides insight into the differences in these domains from different kingdoms of life. While the overall fold of the L-type lectin domain is conserved, differences in the lengths of the carbohydrate-binding loops and significant variations in the Mn 2+ -binding site compared to the Ca 2+ -binding site are observed. Furthermore, the sequence and phylogenetic analyses suggest that the archaeal L-type lectin domain is evolutionarily closer to the plant legume lectins than to its bacterial or animal counterparts. This is the first report of the biochemical, structural, sequence, and phylogenetic analyses of an L-type lectin domain from archaea and serves to enhance our understanding of the species-specific differences and evolution of L-type lectin domains.


  • Organizational Affiliation
    • Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India.

Macromolecule Content 

  • Total Structure Weight: 23.3 kDa 
  • Atom Count: 1,796 
  • Modeled Residue Count: 207 
  • Deposited Residue Count: 209 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
legume lectinA [auth E]209Methanocaldococcus jannaschii DSM 2661Mutation(s): 0 
Gene Names: MJ1396
UniProt
Find proteins for Q58791 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q58791 
Go to UniProtKB:  Q58791
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58791
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPD

Query on MPD



Download:Ideal Coordinates CCD File
B [auth E],
C [auth E],
D [auth E]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E,
F [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN

Query on MN



Download:Ideal Coordinates CCD File
H [auth E]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
G [auth E]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.175 (Depositor), 0.176 (DCC) 
  • R-Value Work:  0.154 (Depositor), 0.154 (DCC) 
  • R-Value Observed: 0.155 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.293α = 90
b = 55.293β = 90
c = 149.417γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-20
    Type: Initial release
  • Version 1.1: 2022-12-14
    Changes: Database references, Derived calculations
  • Version 1.2: 2022-12-21
    Changes: Database references
  • Version 1.3: 2023-03-22
    Changes: Database references
  • Version 1.4: 2023-11-29
    Changes: Data collection, Refinement description