1FSL

FERRIC SOYBEAN LEGHEMOGLOBIN COMPLEXED WITH NICOTINATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 0.158 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structure of ferric soybean leghemoglobin a nicotinate at 2.3 A resolution.

Ellis, P.J.Appleby, C.A.Guss, J.M.Hunter, W.N.Ollis, D.L.Freeman, H.C.

(1997) Acta Crystallogr D Biol Crystallogr 53: 302-310

  • DOI: 10.1107/S0907444997000292
  • Primary Citation of Related Structures:  
    1FSL

  • PubMed Abstract: 
  • Soybean leghemoglobin a is a small (16 kDa) protein facilitating the transport of O(2) to respiring N(2)-fixing bacteria at low free-O(2) tension. The crystal structure of soybean ferric leghemoglobin a nicotinate has been refined at 2.3 A resolution. The final R factor is 15 ...

    Soybean leghemoglobin a is a small (16 kDa) protein facilitating the transport of O(2) to respiring N(2)-fixing bacteria at low free-O(2) tension. The crystal structure of soybean ferric leghemoglobin a nicotinate has been refined at 2.3 A resolution. The final R factor is 15.8% for 6877 reflections between 6.0 and 2.3 A. The structure of soybean leghemoglobin a (143 residues) is closely similar to that of lupin leghemoglobin II (153 residues), the proteins having 82 identical residues when the sequences are aligned. The new structure provides support for the conclusion that the unique properties of leghemoglobin arise principally from a heme pocket considerably larger and more flexible than that of myoglobin, a strongly ruffled heme group, and a proximal histidine orientation more favourable to ligand binding.


    Related Citations: 
    • Crystal Structure of Soybean Ferric Leghaemoglobin a Nicotinate at a Resolution of 3.3 Angstrom
      Ollis, D.L., Appleby, C.A., Colman, P.M., Cutten, A.E., Guss, J.M., Venkatappa, M.P., Freeman, H.C.
      (1983) Aust J Chem 36: 451

    Organizational Affiliation

    School of Chemistry, University of Sydney, NSW, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LEGHEMOGLOBIN AA, B143Glycine maxMutation(s): 0 
Gene Names: LBA
UniProt
Find proteins for P02238 (Glycine max)
Explore P02238 
Go to UniProtKB:  P02238
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02238
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
NIO
Query on NIO

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
NICOTINIC ACID
C6 H5 N O2
PVNIIMVLHYAWGP-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 0.158 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.69α = 90
b = 56.55β = 109.9
c = 57.8γ = 90
Software Package:
Software NamePurpose
PROFFTrefinement
ENRAF-NONIUSdata reduction
PROTEINdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-06-26
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-04-04
    Changes: Data collection, Other
  • Version 1.4: 2018-04-18
    Changes: Data collection