1F5P | pdb_00001f5p

2.9 ANGSTROM CRYSTAL STRUCTURE OF LAMPREY HEMOGLOBIN THAT HAS BEEN EXPOSED TO CARBON MONOXIDE.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.256 (Depositor) 
  • R-Value Work: 
    0.206 (Depositor), 0.211 (DCC) 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Crystalline ligand transitions in lamprey hemoglobin. Structural evidence for the regulation of oxygen affinity.

Heaslet, H.A.Royer Jr., W.E.

(2001) J Biological Chem 276: 26230-26236

  • DOI: https://doi.org/10.1074/jbc.M101391200
  • Primary Citation Related Structures: 
    1F5O, 1F5P

  • PubMed Abstract: 

    The hemoglobins of the Sea Lamprey (Petromyzon marinus) exist in an equilibrium between low affinity oligomers, stabilized by proton binding, and higher affinity monomers, stabilized by oxygen binding. Recent crystallographic analysis revealed that dimerization is coupled with key changes at the ligand binding site with the distal histidine sterically restricting ligand binding in the deoxy dimer but with no significant structural rearrangements on the proximal side. These structural insights led to the hypothesis that oxygen affinity of lamprey hemoglobin is distally regulated. Here we present the 2.9-A crystal structure of deoxygenated lamprey hemoglobin in an orthorhombic crystal form along with the structure of these crystals exposed to carbon monoxide. The hexameric assemblage in this crystal form is very similar to those observed in the previous deoxy structure. Whereas the hydrogen bonding network and packing contacts formed in the dimeric interface of lamprey hemoglobin are largely unaffected by ligand binding, the binding of carbon monoxide induces the distal histidine to swing to positions that would preclude the formation of a stabilizing hydrogen bond with the bound ligand. These results suggest a dual role for the distal histidine and strongly support the hypothesis that ligand affinity in lamprey hemoglobin is distally regulated.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA.

Macromolecule Content 

  • Total Structure Weight: 101.61 kDa 
  • Atom Count: 7,160 
  • Modeled Residue Count: 894 
  • Deposited Residue Count: 894 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HEMOGLOBIN V
A, B, C, D, E
A, B, C, D, E, F
149Petromyzon marinusMutation(s): 0 
UniProt
Find proteins for P02208 (Petromyzon marinus)
Explore P02208 
Go to UniProtKB:  P02208
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02208
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



Download:Ideal Coordinates CCD File
G [auth A]
I [auth B]
K [auth C]
M [auth D]
O [auth E]
G [auth A],
I [auth B],
K [auth C],
M [auth D],
O [auth E],
Q [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
CMO

Query on CMO



Download:Ideal Coordinates CCD File
H [auth A]
J [auth B]
L [auth C]
N [auth D]
P [auth E]
H [auth A],
J [auth B],
L [auth C],
N [auth D],
P [auth E],
R [auth F]
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.256 (Depositor) 
  • R-Value Work:  0.206 (Depositor), 0.211 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.5α = 90
b = 96.2β = 90
c = 145.1γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-06-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations