2OFM

1.11 A Crystal Structure of Apo Nitrophorin 4 From Rhodnius Prolixus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.11 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Apo-nitrophorin 4 at atomic resolution.

Amoia, A.M.Montfort, W.R.

(2007) Protein Sci 16: 2076-2081

  • DOI: https://doi.org/10.1110/ps.072981907
  • Primary Citation of Related Structures:  
    2OFM

  • PubMed Abstract: 

    The nitrophorins from Rhodnius prolixus, the kissing bug, are heme-containing proteins used for the transport of nitric oxide to aide the insect in obtaining a blood meal. The Rhodnius nitrophorins display an eight-stranded antiparallel beta-barrel motif, typical of lipocalins, with a histidine-linked heme in the open end of the barrel. Heme is stabilized in the ferric state and highly distorted, displaying a ruffled conformation that may be of importance in the setting of the reduction potential. To help in understanding the means by which the protein matrix, an inherently soft material, is able to distort the heme from its low-energy planar conformation, we have determined the crystal structure of apo-nitrophorin 4-1.1 A resolution. Removal of the heme from nitrophorin 4 has very little effect on its structure: The heme binding cavity remains open and the loops near the cavity entrance respond to lower pH in the same manner as the intact protein. We conclude that the general stability of the lipocalin fold and apparent rigidity of the beta-barrel provide the means for distorting the heme cofactor.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, Arizona 85721, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrophorin-4A [auth X]184Rhodnius prolixusMutation(s): 0 
UniProt
Find proteins for Q94734 (Rhodnius prolixus)
Explore Q94734 
Go to UniProtKB:  Q94734
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ94734
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
B [auth X]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.11 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.47α = 90
b = 42.816β = 94.71
c = 52.72γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2007-12-18 
  • Deposition Author(s): Amoia, A.M.

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description